How Does an SEO Company Optimize Website Structure for Better Rankings?

An SEO company optimizes site structure in five steps. It crawls and inventories every indexable URL, maps those URLs into a shallow hierarchy so important pages sit a few clicks from the homepage, rebuilds internal links around hub pages, aligns URLs and breadcrumbs with that hierarchy, and stops pagination and filter URLs from competing with the category pages they belong to. Structure work assumes Google can already crawl the site.

If Google cannot reach or index your pages at all, that is a separate problem to fix first; see how an SEO company improves website crawlability and indexing.

Step 1: Inventory the Site Before Any Redesign

Every structure project should start with a content inventory. The agency crawls the existing site, for example with Screaming Frog or Sitebulb, exports every indexable URL, and maps each one against the keyword and topic research. The output is a target hierarchy, which for a small or mid-size site can be three levels below the homepage: category, subcategory, then product or article.

What the hierarchy looks like depends on the platform:

• WordPress organizes content by categories and tags. When tags grow into a second, uncontrolled taxonomy, they can create archive pages that duplicate the category pages and compete with them. The fix is to choose one primary taxonomy for the hierarchy, then decide the other taxonomy’s archive pages one at a time: keep those that earn clicks or links and serve a purpose of their own, and noindex or merge the rest.
• Shopify and similar e-commerce platforms use collections. Collections built on automated tag rules can generate overlapping URLs such as /collections/red-shoes, /collections/shoes-on-sale and /collections/mens-shoes-red that target versions of the same query. The fix is to consolidate collections around measured search demand.
• Custom or headless builds have no default taxonomy, so the hierarchy has to be decided in the URL routing and navigation configuration.

Step 2: Find the Pages Nothing Links To

An orphan page is one that cannot be reached by following internal links from the start page. Screaming Frog’s orphan page tutorial says a crawl that only follows links cannot find them, so additional URL sources are needed, namely XML sitemaps and the Google Analytics and Search Console integrations. After the crawl, the agency runs Crawl Analysis, and the Orphan URLs filters under the Sitemaps, Analytics and Search Console tabs fill in. Screaming Frog adds that pages without internal links “won’t be passed internal PageRank,” even if they are still indexed through sitemaps or external links.

Each orphan then needs a decision. Pages still earning clicks in Search Console get a contextual link from the most relevant strong page. Low-value pages are not linked back in, and each type gets its own treatment: thank-you pages are noindexed; dead campaign pages are redirected to a live page that covers the same offer, or return a 404 or 410 when none does; and duplicates get a canonical or a redirect to the main version.

Step 3: Rebuild Internal Links Around Hub Pages

The 2024 Web Almanac found that pages on the top 1,000 sites carried a median of 129 internal links on mobile, up from 106 in 2022, against 41 across all sites. The Almanac suggests this might be because the most visited sites are bigger and invest in large navigation menus. Those numbers describe how heavily big sites link, template links included; they do not show that more links cause higher rankings. Set the number of links per page from your hierarchy, not from the median.

A working internal link plan includes:

• Hub pages that link to every subpage they are responsible for, and subpages that link back to the hub, not only sideways to siblings.
• Contextual links in body copy whose anchor text names the target page’s topic.
• A scheduled review, for example each quarter, that adds links from older pages to newer ones. Check whether your older posts link to anything published after them; if they do not, this review fixes it.
• Pruning instead of capping. Remove sitewide or low-value links that add nothing for the reader rather than setting an arbitrary maximum per page.

Step 4: Decide Which Pages Belong in the Same Silo

A topic silo groups the pages for one subject under a shared parent, with the parent linking to every child and children linking back. The useful rule is about membership: group pages under one parent only when they answer queries from the topic family that parent targets. If a page fits two parents, place it under the one whose query it supports most directly and add a contextual link to the other. A rigid “never link outside the silo” policy cuts links readers would use.

Step 5: Align URLs and Breadcrumbs With the Hierarchy

URL rules the agency should enforce:

• Descriptive, readable paths: /services/local-seo/ rather than /services/?id=4827.
• Depth that matches the hierarchy: /shoes/running/trail/ for a subcategory.
• A URL-by-URL redirect map before any URL changes. Every old URL gets a 301 to its specific new equivalent, never a blanket redirect to the homepage; a URL with no real equivalent returns a 404 or 410 instead, as Google’s site move guide advises for content that is not moving. A restructure without that map can cause a temporary or lasting ranking drop.
• Short, stable slugs. Once a URL has earned links, changing it without a redirect discards that equity. Where internal links, navigation and breadcrumbs can express the hierarchy, leave working URLs as they are; change them only when the gain outweighs the risk of a migration.

Breadcrumbs give users a way up the hierarchy and give Google a second statement of how the site is organized. Google’s breadcrumb documentation recommends breadcrumbs that “represent a typical user path to a page, instead of mirroring the URL structure.” It also says the last item does not need an item URL; if it is left out, Google uses the URL of the containing page. The breadcrumb display is a desktop feature: the same documentation says it “is available on desktop in all regions and languages where Google Search is available.” Google’s Search Central changelog records that on January 22, 2025 it limited breadcrumbs to desktop results, because they get truncated on smaller screens.

An example with placeholder URLs, in the JSON-LD format Google documents:

{
  "@context": "https://schema.org",
  "@type": "BreadcrumbList",
  "itemListElement": [{
    "@type": "ListItem",
    "position": 1,
    "name": "Services",
    "item": "https://example.com/services"
  },{
    "@type": "ListItem",
    "position": 2,
    "name": "Local SEO",
    "item": "https://example.com/services/local-seo"
  },{
    "@type": "ListItem",
    "position": 3,
    "name": "Google Business Profile Optimization"
  }]
}

Pagination and Filters Without Competing Pages

Paginated archives and filter combinations on category pages can generate large numbers of near-duplicate URLs. Google treats them differently, and so should the fix.

Problem	What it generates	What Google's documentation says to do
Pagination (page 2, 3 of an archive or category)	A sequence of similar pages	Give each page its own URL and its own canonical; do not canonicalize every page to page 1. Google no longer uses the old rel=next and rel=prev markup, and pages in a sequence may share titles and descriptions.
Faceted navigation (size, color, price filters)	Large numbers of filter-combination URLs	If you do not need filtered URLs indexed, disallow their parameters in robots.txt or move filters into URL fragments, which Google Search generally does not support in crawling and indexing. Canonical tags and nofollow on filter links are, in Google's words, "generally less effective in the long term".

The table follows Google’s pagination documentation and its faceted navigation guide.

Keep indexable filter URLs only for combinations with their own search demand, such as “men’s running shoes,” and not “men’s running shoes size 10 in blue under $50.”

When Structure Work Comes First

Structure fixes belong in the first phase when the audit finds money pages buried deep in the site or left without internal links, because new content and new links both depend on where those pages sit. When the hierarchy is already sound, structure is maintenance alongside the on-page work in how an SEO company improves a website’s on-page SEO. How structural findings are scored against speed and indexing issues is part of a technical SEO audit.

What to Ask For Before You Approve Structure Work

Ask the agency for four deliverables before any change goes live:

1. The crawl inventory, with each URL’s planned place in the new hierarchy.
2. The redirect map for every URL that changes.
3. The internal link plan for hub pages.
4. The list of filter or tag URLs that will stay indexable, and why.

If the agency cannot produce these, the project is a redesign with SEO language attached. After launch, compare the orphan count and the number of indexed pages in Search Console with the figures before the change.