SEO Silo Structure: Why It Makes No Sense (And What to Do Instead)

In this article, you’ll learn what SEO silo structure is, why so many SEOs still recommend it, what’s fundamentally wrong with the approach, and what to do instead. You’ll also learn how your site’s architecture affects visibility in AI search engines like ChatGPT, Perplexity, and Gemini—and how to structure your site so it performs well across both traditional and AI-powered search.

But first, let’s make sure we’re on the same page about what siloing actually means.

What Is Silo Structure in SEO?

Silo structure in SEO is a way of organizing a website where you group content into isolated, topic-based sections—and only allow internal links within each section. Each section (or “silo”) has a main page at the top, with supporting pages underneath, all interlinked to each other.

The critical rule: content in one silo does not link to content in another silo.

For example, imagine a fitness website with three silos: “Strength Training,” “Yoga,” and “Nutrition.” Under the silo model, your article about post-workout meals would only link to other nutrition pages—never to a strength training article about muscle recovery, even if the connection is obvious and useful for the reader.

That’s why it’s called a “silo.” The content is literally sealed off from the rest of the site.

The concept was first popularized by Bruce Clay in the early 2000s as a way to help search engines understand topical relevance. The logic was straightforward: if you keep all your “Nutrition” content tightly grouped and interlinked, search engines will recognize your authority on that topic.

At the time, search engines were far less sophisticated. Grouping content into tight clusters and restricting cross-links was a reasonable tactic. But search has changed—and the advice hasn’t kept up.

Why Is Siloing So Popular?

Despite its flaws, siloing remains one of the most widely recommended types of SEO site architecture. A quick search for “silo structure SEO” returns thousands of articles endorsing the approach.

The reason is the perceived benefits, which typically fall into three categories.

1. It Helps Google Find Your Pages

Internal links are one of the primary ways Google discovers new pages. Siloing creates a logical hierarchy with consistent internal linking, which makes it easier for search engines to crawl and index your content.

This is a real benefit. But it’s not unique to siloing. Any well-structured site with consistent internal linking achieves the same thing.

2. It Can Boost Rankings

There are two reasons siloing is believed to improve rankings.

Better PageRank flow. PageRank is Google’s system for scoring a page based on the quantity and quality of pages linking to it. Backlinks bring PageRank into your site; internal links distribute it around your site. Since all pages in a silo are interlinked, PageRank flows freely between them. If one page in the silo earns strong backlinks, that authority gets shared with the other pages in the silo through internal links.

More contextual internal links. Silos group related content together. This means the internal links between pages within a silo are usually topically relevant—and often use relevant anchor text. Both of these signals help Google understand what a page is about.

Google’s John Mueller has confirmed that internal linking provides contextual signals. In a Webmaster Hangout, he explained that Google gets context from both the anchor text of internal links and from understanding where pages are linked within the site’s overall structure.

For example, if a page receives internal links with anchors like “best CRM for small businesses,” “HubSpot vs Salesforce,” and “CRM pricing comparison,” Google can infer the page is about CRM software—even before reading the content itself.

3. It Creates a Good User Experience

Internal links help users navigate your site. Siloing places topically related pages close together, which can make it easier for visitors to find related content without jumping between unrelated sections.

This is true. But again, it’s not exclusive to siloing. Any logical grouping of content achieves this. You don’t need to prohibit cross-silo links to keep related content close together.

What’s the Problem With Silo Structure?

Given those benefits, you might wonder what’s wrong with siloing.

Here’s the problem: forbidding internal links between silos is counterproductive for both SEO and users.

Every perceived benefit of siloing can be achieved without the restriction on cross-silo links. And that restriction actively hurts your site.

The Cross-Link Problem

Let’s say you run a home improvement website with three silos: “Kitchen Remodels,” “Bathroom Remodels,” and “Flooring.”

Neat and tidy. But what happens when you publish a guide about “Best Tile for Kitchens and Bathrooms”? Under strict siloing, that guide can only live in one silo. It can link to either kitchen content or bathroom content—but not both. And your flooring silo, which has a detailed page on tile types, can’t link to it at all.

This makes no sense. The reader looking at tile flooring options would benefit from seeing kitchen and bathroom installation guides. The reader planning a kitchen remodel would benefit from seeing flooring options. These are contextually relevant connections that help both users and search engines.

But siloing says you can’t make them.

Gael Breton from Authority Hacker put it directly: as long as it contextually makes sense to link to another page on your site, you should do it. The idea of “keeping link juice in the silo” is outdated and unhelpful.

And here’s the thing: once you start adding cross-silo links wherever they’re relevant, you’re no longer siloing. You’re just using a traditional pyramid site architecture—which is what most SEO professionals recommend anyway.

John Mueller has endorsed this approach, explaining that a top-down or pyramid structure helps Google understand the context of individual pages within a site far better than isolated silos.

Siloing Restricts PageRank Flow

Ironically, one of the perceived benefits of siloing—better PageRank flow—is actually undermined by the silo model itself.

When you restrict internal links to within a silo, you’re preventing PageRank from flowing to relevant pages in other silos. If your “Kitchen Remodels” silo earns a bunch of high-quality backlinks, that authority stays trapped in the kitchen silo. Your equally important “Flooring” and “Bathroom” silos get none of it—even though they’re topically related and would benefit from the boost.

A pyramid structure with free cross-linking solves this. PageRank still flows naturally through the hierarchy, but it also flows to relevant pages across the site—wherever a contextual link exists.

Siloing Ignores How Users Actually Browse

Real users don’t navigate in silos. They follow their curiosity. A visitor reading about kitchen countertops might want to learn about backsplash tiles next, then jump to flooring options, then check out a budget calculator for their remodel. Siloing forces them to stay in one lane, which creates friction and increases bounce rates.

Good site architecture should mirror how people actually think about topics—not how a rigid taxonomy diagram looks on a whiteboard.

Best Practices for Site Structure

With silo structure out of the way, let’s look at what actually works for organizing a website—both for traditional SEO and for AI search visibility.

1. Use a Pyramid Structure

A pyramid structure puts your most important content at the top, followed by your second most important content, and so on. Most well-built websites already follow this pattern.

Here’s what a home furniture website might look like:

The homepage links to main categories. Main categories link to subcategories. Subcategories link to individual product or content pages. And every level links back up.

This structure delivers three clear benefits:

Easy to navigate. Visitors start on the homepage, pick a category, and dig deeper. The path is intuitive.

Good PageRank flow. Homepages tend to earn the most backlinks. Placing your most important content close to the homepage—just one or two clicks away—ensures it gets the strongest share of that authority.

Contextual internal links. Categories naturally link to their subcategories and vice versa. The linking structure itself provides topical context to search engines.

Notice that these are the same benefits people attribute to siloing. The difference is that a pyramid structure achieves them without the downside of restricting cross-section links.

How Pyramid Structure Affects AI Search

Here’s something most articles about site architecture miss entirely: your site structure doesn’t just affect Google rankings. It affects how AI search engines understand and cite your content.

AI models like ChatGPT, Perplexity, Claude, and Gemini pull information from web pages to generate their answers. When your site has a clear pyramid structure, these models can better understand the relationship between your pages—which makes it more likely they’ll cite your content accurately and in the right context.

A messy, flat, or siloed structure makes it harder for AI crawlers to understand your site’s topical focus. Pages that are isolated in silos may not get crawled as thoroughly by AI models, which typically follow links to discover content. If a page can only be reached through a narrow set of internal links, it’s less likely to be discovered and cited.

With Analyze AI, you can see exactly which of your pages AI engines are citing—and which ones they’re ignoring. The Landing Pages report shows which pages receive AI-referred traffic, broken down by which AI engine sent the visitor and how engaged those visitors are.

If you notice that only a handful of pages get cited while others are invisible, it’s often a structural problem. Pages buried deep in a rigid silo or lacking cross-links from authoritative pages on your site are less likely to surface in AI-generated answers.

2. Internally Link Wherever It’s Relevant

The main problem with silo structure is that it blocks relevant internal linking opportunities outside of the silo. A pyramid structure with no such restriction solves this completely.

For example, let’s say you have a “blue velvet sofa” product page in your Living Room section and a “blue velvet dining chairs” product page in your Dining Room section. These pages are in different areas of the site, but they’re clearly related—same style, same material, same buyer intent.

Under a silo model, you couldn’t link between them. Under a pyramid structure, you simply add the link wherever it makes sense. This is better for users (who might want to furnish their whole home in the same style) and better for your bottom line (cross-selling opportunity).

How to Find Internal Linking Opportunities

Finding relevant internal linking opportunities manually is time-consuming, especially on large sites. There are two practical approaches.

Use an internal link opportunities tool. Most SEO audit tools include a feature that crawls your site and suggests internal links you’re missing. These tools look for pages that mention a keyword you’re targeting on another page, then suggest you link them.

For example, the tool might find that your blog post about “home office design” mentions “standing desks” but doesn’t link to your standing desk product page. That’s a missed opportunity.

Search for keyword mentions across your site. If you don’t have access to an audit tool, you can use Google’s site: operator to find mentions of a keyword on your own domain. Search for site:yourdomain.com "standing desk" to find every page that mentions standing desks, then add internal links to your standing desk page from each of those pages.

Either way, the goal is the same: find every contextually relevant place on your site where you could add an internal link—and add it. Don’t let artificial silo boundaries stop you.

You can use the Analyze AI Broken Link Checker to make sure your existing internal links are actually working. Broken internal links waste PageRank and create dead ends for both users and crawlers.

What This Means for AI Search Visibility

Internal links don’t just help Google. They help AI models map the relationships between your pages.

When ChatGPT or Perplexity crawls your site, it follows internal links to understand which pages are related and how your content fits together. Cross-links between topically related pages—even across different sections of your site—help these models build a richer understanding of your expertise.

This matters because AI search engines tend to cite sources that demonstrate broad, interconnected expertise on a topic. If your content about “standing desks” only links to other pages about desks (strict silo), an AI model might not realize you also have expert content about ergonomics, home office design, and back pain prevention. But if those pages are cross-linked, the model can see the full picture—and is more likely to cite you across a range of related queries.

You can track exactly which sources AI engines cite in your space using Analyze AI’s Sources dashboard. It shows you the top cited domains, the types of content being cited (blogs, product pages, reviews), and how the citation landscape shifts over time.

This data tells you which domains are winning citations in your space. If a competitor with strong cross-linking is getting cited more than you, it’s a signal that your internal linking structure might be holding you back.

3. Create Content Hubs for Blog Content

Blog content has a unique structural problem: it’s typically published in reverse chronological order. Your most recent post sits on top; everything else gets pushed deeper into archive pages. There’s no topical hierarchy by default.

This is bad for SEO because Google may struggle to understand how your blog posts relate to each other. And it’s bad for users because they have to hunt through a timeline to find related content.

Content hubs solve this. A content hub is a collection of related content, organized around a central “pillar” or hub page that links out to supporting pages—all of which link back to the hub and to each other.

Content hubs are similar to silos in that they group related content together with internal links. But there’s one major difference: you’re free to link between content hubs.

For example, imagine you have two content hubs: one about “Content Marketing” and one about “SEO.” Your post about “keyword research” lives in the SEO hub, but it’s directly relevant to your content marketing hub too—because keyword research is how you find topics to write about. Under a silo model, you couldn’t make that connection. With content hubs, you simply link between them wherever it’s useful.

This gives you the best of both worlds: related content is grouped and interlinked (so search engines understand your topical focus), but you can also link between hubs wherever it makes sense (so you don’t miss relevant contextual opportunities).

Recommended reading: What Is Keyword Clustering and How to Do It

How to Build a Content Hub

Here’s a step-by-step approach:

Step 1: Pick a core topic. This should be a broad topic that you cover extensively on your blog. Examples: “Link Building,” “Email Marketing,” “Product-Led Growth.”

Step 2: Identify your hub page. This is your most comprehensive piece on the core topic. It should provide a thorough overview and link out to more detailed supporting pages. If you don’t have a good hub page yet, create one.

Step 3: Map your supporting content. Go through your existing blog posts and identify everything related to the core topic. These become the “spokes” of your hub.

Step 4: Interlink everything. The hub page links to every supporting page. Every supporting page links back to the hub. And supporting pages link to each other wherever there’s a relevant connection.

Step 5: Add cross-hub links. Look for opportunities to link between content hubs. Your “Email List Building” post in the Email Marketing hub might reference organic traffic—link it to your SEO hub. Your “SEO content strategy” post might discuss content promotion—link it to your Social Media hub.

Why Content Hubs Work for AI Search

Content hubs are especially powerful for AI search visibility because they mirror how AI models evaluate topical authority.

When an AI model processes a query like “best email marketing strategies for ecommerce,” it doesn’t just find one page and cite it. It looks for sources that demonstrate deep, interconnected expertise on the topic. A site with a well-built email marketing content hub—where the hub page links to detailed supporting content about segmentation, automation, deliverability, and A/B testing—signals exactly that kind of depth.

AI models also follow links to discover related content. A content hub with strong internal linking gives the model more material to draw from, which increases the chances that one of your pages gets cited in the generated answer.

You can validate this by using Analyze AI’s Prompts dashboard to track how your brand appears across different AI-generated responses. Set up tracked prompts related to your content hub topics and monitor your visibility, position, and which competitors appear alongside you.

If your content hub is well-structured, you should see your brand appearing consistently across related prompts. If not, it might be a signal that your hub’s internal linking is weak, or that the hub page itself isn’t comprehensive enough to serve as a definitive resource.

4. Make Sure Important Content Isn’t Too Deep

Content depth—how many clicks it takes to reach a page from your homepage—matters for both SEO and AI search.

It’s a common misconception that search engines can’t find deep content. They can, as long as it’s internally linked. Google will crawl and index a page buried seven clicks deep if there’s a link path to it.

But there’s a catch: Google may not prioritize crawling or indexing deep content because it assumes pages far from the homepage are less important. If a page is buried five or six clicks deep, Google might crawl it less frequently, which means updates take longer to reflect in search results—and the page may struggle to rank for competitive terms.

The same principle applies to AI search. AI crawlers follow links to discover content. The deeper a page is buried, the less likely an AI model is to find it, index it, and ultimately cite it in its generated answers.

How to Check Content Depth

You can check how deep your content is using a site audit tool. Most SEO audit tools include a “site structure” or “depth” report that shows you how many clicks each page is from the homepage (or from whatever page you set as the crawl seed).

Look for important pages that are four or more clicks deep. If you find any, add internal links to them from higher-level pages. This brings them closer to the surface and signals to both Google and AI crawlers that these pages matter.

For example, if your best-performing blog post about “how to use keywords in SEO” is buried at depth 4 because it’s only linked from an archive page, add an internal link to it from your main SEO hub page (depth 1 or 2). This immediately reduces its depth and increases its chances of being crawled, indexed, and cited.

5. Use Clean, Descriptive URL Structures

This is a best practice that’s often overlooked in discussions about silo vs. pyramid structures, but it matters for both SEO and AI search.

Your URL structure should reflect your site’s hierarchy in a way that’s readable to both humans and machines. A clean URL structure tells search engines (and AI crawlers) exactly where a page fits within your site.

Good URL structure:

• yoursite.com/living-room/sofas/blue-velvet-sofa

• yoursite.com/blog/seo/internal-linking-guide

Bad URL structure:

• yoursite.com/p?id=4827&cat=3

• yoursite.com/blog/2024/03/15/post-title-here

The good examples communicate hierarchy: this page is about a blue velvet sofa, which lives in the sofas subcategory, which lives in the living room category. Search engines and AI models can parse that structure and use it as a contextual signal.

The bad examples communicate nothing. A query string tells no one what the page is about. And a date-based URL structure suggests chronological organization rather than topical organization—which undermines the whole point of building a pyramid or hub structure.

One caveat: don’t force URL depth to match silo depth. It’s fine for a blog post to live at yoursite.com/blog/internal-linking-guide rather than yoursite.com/blog/seo/link-building/internal-linking-guide. What matters is that the URL is descriptive and readable, not that it mirrors a five-level taxonomy.

6. Submit an XML Sitemap

An XML sitemap is a file that lists all the pages on your site you want search engines to know about. It doesn’t replace good internal linking, but it acts as a safety net to ensure nothing gets missed.

This is especially important for large sites where some pages might be buried deep or orphaned (not linked from anywhere else on the site). The sitemap gives search engines a direct list of every page that matters.

For AI search, sitemaps play a slightly different role. Some AI crawlers use sitemaps to discover content more efficiently. Having a well-maintained sitemap ensures these crawlers can find your content even if your internal linking isn’t perfect.

If your site runs on WordPress, most SEO plugins (Yoast, Rank Math, All in One SEO) generate and update your sitemap automatically. If not, you can use free tools or generate one manually.

You can also create an LLM.txt file for your website, which is essentially a sitemap designed specifically for AI models. It tells AI crawlers which pages on your site are most important and what each page is about—making it easier for models to cite the right content in the right context.

How to Audit Your Site Structure for Both SEO and AI Search

Knowing the best practices is one thing. Applying them to an existing site is another. Here’s a practical audit process you can follow.

Step 1: Crawl Your Site

Use a site audit tool to crawl your entire website. This gives you a map of your current site structure, including every page, every internal link, and the depth of each page.

Pay attention to three things during the crawl:

Orphan pages. These are pages with no internal links pointing to them. They’re invisible to both users and crawlers. Either add internal links to them or remove them if they’re not valuable.

Deep pages. Any important page at depth 4 or higher needs to be brought closer to the surface through additional internal links.

Broken links. Internal links that point to 404 pages waste PageRank and create dead ends. Fix or remove them. You can use the Analyze AI Broken Link Checker for a quick check.

Step 2: Map Your Content to Topics

Once you have a crawl, group your content by topic. This is where you identify potential content hubs.

Go through your blog posts and pages and tag each one with a primary topic. Then look for natural groupings. If you have 15 posts about “email marketing,” that’s a content hub. If you have 20 posts about “keyword research,” that’s another hub.

Use keyword clustering to identify which pages should be grouped together based on the keywords they target. Pages targeting semantically related keywords should be in the same content hub.

Step 3: Identify Cross-Link Opportunities

With your content mapped to topics, look for cross-link opportunities between hubs. Ask yourself: “Does any page in Hub A mention a topic covered in detail by a page in Hub B?”

If yes, add the link.

You can also use the SERP Checker or Keyword Rank Checker to find pages that are ranking on page 2 or 3 of Google. These “striking distance” pages often benefit the most from additional internal links, which can provide the ranking boost they need to reach page 1.

Step 4: Check Your AI Search Visibility

This is the step most site structure audits miss. After optimizing your structure for traditional SEO, check how your site performs in AI search.

With Analyze AI, you can see a complete picture of your AI search presence. The Overview dashboard shows your brand’s visibility across all major AI engines, your sentiment score, and how you compare to competitors.

Analyze AI Overview dashboard showing brand visibility percentage, sentiment score, top AI channel, leading competitor, and visibility/sentiment trend charts over time

If your visibility is low or declining, it may point to structural issues. Pages that aren’t well-linked, content that’s buried too deep, or a missing content hub around a key topic can all reduce your chances of being cited in AI-generated answers.

The Competitors view shows you which brands AI engines mention alongside yours—and how often. If a competitor with a better site structure is getting mentioned more frequently, that’s a strong signal that your architecture needs work.

Analyze AI Competitors dashboard showing tracked competitors with their mention counts and last seen dates across AI engines

Step 5: Monitor and Iterate

Site structure isn’t a one-time project. As you publish new content, add new products, or expand into new topics, your structure needs to evolve.

Set a quarterly reminder to re-crawl your site, check for new orphan pages, review content depth, and update your content hubs. And keep monitoring your AI search visibility in Analyze AI to catch any drops early.

The Analyze AI Weekly Emails feature sends you a summary of your AI visibility changes every week, so you don’t have to manually check the dashboard. If a structural change on your site causes a drop in AI citations, you’ll know quickly.

Recommended reading: How To Get Mentioned in AI Search (From 65k Citations Data)

Silo Structure vs. Pyramid Structure vs. Content Hubs: A Quick Comparison

The table makes it clear: pyramid structures and content hubs deliver every benefit of siloing without the downsides. There’s no practical scenario where strict siloing outperforms a pyramid structure with content hubs and free cross-linking.

How AI Search Changes the Site Structure Conversation

Most discussions about site structure focus exclusively on Google. But search is evolving. AI-powered search engines—ChatGPT, Perplexity, Claude, Gemini, Microsoft Copilot—now represent a growing share of how people find information online.

This doesn’t mean SEO is dead. Far from it. AI search is an evolution of SEO, not a replacement for it. The fundamentals that have always mattered—quality content, clear structure, strong internal linking, topical authority—still matter. What’s changed is that those fundamentals now need to be legible to AI models, not just to Google’s crawler.

Here’s what that means for site structure specifically.

AI Models Follow Links

AI crawlers discover your content by following links, just like Googlebot. A well-linked pyramid structure with content hubs gives AI models more entry points to discover your content and more context to understand how your pages relate to each other.

Siloing restricts these entry points. Fewer cross-links means fewer paths for AI crawlers to follow, which means less of your content gets discovered and cited.

AI Models Evaluate Source Authority Across Topics

When an AI model answers a query, it doesn’t just find one matching page. It evaluates potential sources based on depth, breadth, and credibility. A site that demonstrates interconnected expertise across related topics—the kind of expertise that cross-linked content hubs naturally showcase—is more likely to be cited than a site with isolated silos.

You can see which sources AI engines are citing in your industry using the Analyze AI Sources dashboard. This shows you the top cited domains and the types of content (blogs, product pages, documentation) that get cited most often. Use this data to understand what kind of structure and content the winning domains have—and build your own site accordingly.

AI Traffic Is Measurable

One of the biggest advantages of treating AI search as an organic channel is that you can measure it. Analyze AI connects to your GA4 data and shows you exactly how much traffic comes from AI engines, which engines send it, and which pages receive it.

This means you can tie structural improvements directly to results. Restructure a content hub, add cross-links, fix orphan pages—then watch whether your AI-referred traffic increases. That’s a feedback loop that helps you make better decisions over time.

Recommended reading: How to Rank on ChatGPT (Based on 65,000 Citation Data)

Final Thoughts

Organizing your content makes sense. Siloing your content doesn’t.

All siloing does is prevent you from internally linking your content from relevant, contextual locations across your site. It restricts PageRank flow, limits the user experience, and reduces your chances of being cited by AI search engines.

The better approach is straightforward:

Organize your site in a pyramid structure. Put your most important content at the top, with supporting content beneath it.

Group related blog content into content hubs. Give your blog posts topical context by organizing them around pillar pages.

Internally link wherever it makes contextual sense. Don’t let arbitrary silo boundaries stop you from connecting related pages.

Keep important content close to the surface. Don’t bury your best content five clicks deep.

Monitor your AI search visibility. Use Analyze AI to track which pages get cited by AI engines, identify structural gaps, and measure the impact of your improvements.

This approach works for Google and for AI search. It’s better for users. It’s better for SEO. And it’s the way the best-structured sites on the web have always worked—long before anyone called it a “silo.”