If you run SEO for a huge site—think tens of thousands of URLs, complicated navigation, and lots of moving parts—technical issues aren’t just annoyances. They’re money pits. This guide is for in-house SEOs, agencies, and anyone wrangling big enterprise sites who wants to use SEMrush for a proper technical audit. No vague hand-waving—just what to focus on, what to skip, and where SEMrush shines (or falls short).
1. Prep: Don’t Just Crawl Blind
Before you fire up any tool, know what you’re dealing with. Large sites can be tricky, and SEMrush is powerful, but not magic.
- Map out your site: Get a list of major domains, key subdomains, and any “off-in-the-corner” sections. Surprise sections waste crawl budget.
- Talk to devs or product teams: Find out about staging sites, password-protected areas, or legacy content.
- Set your audit goals: Are you worried about crawlability? Duplicate content? Index bloat? Security? Pick your priorities.
Pro Tip: If your site’s pushing 100k+ URLs, SEMrush’s limits can bite. Their upper crawl limit is 1 million pages per project, but performance can lag way before that. For true monsters, you might supplement with other crawlers (Screaming Frog, Sitebulb).
2. Set Up Your SEMrush Project for Scale
Once you’re clear on your site’s shape, it’s time to get SEMrush ready.
- Create a new Project in SEMrush for your main domain.
- Configure Site Audit settings:
- Crawl scope: Use “Subdomains” if your site spans multiple ones (e.g., blog.domain.com, shop.domain.com).
- Limit crawl budget: Don’t nuke your quotas or crash your site. Start with 10,000-50,000 pages for your first crawl if you’re unsure.
- Authentication: If parts of your site are behind logins, set up credentials.
- Custom robots.txt: SEMrush respects robots.txt, but you can override it in settings if you want to test blocked areas.
What to skip: SEMrush offers a ton of “Integrations” (GA, GSC, Trello, etc.). For technical audits, most aren’t needed. You want crawl data, not dashboards.
3. Run Your Initial Crawl—And Expect It to Take a While
Big sites take time to crawl. SEMrush does a decent job throttling requests, but don’t expect instant results.
- Monitor the crawl: If it drags or fails, check your server logs (or ask IT) to see if the bot’s getting blocked or rate-limited.
- Watch for dead ends: Massive parameterized URLs or session IDs can blow up your crawl. SEMrush will show you if it’s chasing its own tail.
- Pause and tweak: If the crawl is snagging, stop and adjust settings. Don’t just “let it run”—that can waste hours.
Honest take: For sites with lots of JavaScript or client-side rendering, SEMrush’s crawler isn’t as advanced as some others. It’ll get stuck on heavy JS, so don’t trust the results blindly if your site is all React or Angular.
4. Prioritize the Technical Issues That Matter
Once the crawl’s done, SEMrush throws a mountain of issues at you. Not all are equally important.
Focus on These First:
-
Crawlability & Indexability:
- Broken internal links
- Orphaned pages
- Overly deep pages (buried more than 3-4 clicks from home)
- Robots.txt blocks or “noindex” misfires
-
Duplicate Content:
- Identical or near-identical pages (common with e-commerce filters, faceted nav)
- Canonical tag errors
-
Site Performance:
- Slow-loading pages (SEMrush reports this, but double-check with real tools like PageSpeed Insights)
-
Sitemap & Robots.txt:
- Missing or outdated XML sitemaps
- Sitemap doesn’t match what’s indexable
-
HTTPS & Security:
- Mixed content (HTTP resources on HTTPS pages)
- Expired or invalid certificates
What to ignore: SEMrush will flag tons of “low word count” warnings, “missing meta descriptions,” or “long title tags.” For enterprise, these are rarely urgent unless you’re seeing real ranking or CTR issues.
Pro Tip: Don’t get obsessed with SEMrush’s “Site Health” score. It’s a nice benchmark, but Google doesn’t care about it. Fix what matters for users and bots.
5. Dig Into Crawl Depth and Internal Linking
On big sites, crawl depth kills. If important pages are buried five clicks deep, Google may never see them.
- Check the “Internal Linking” report for pages with few/no inbound links.
- Look for “Orphaned Pages”—these exist but aren’t linked from anywhere else. Sometimes they’re old landing pages, sometimes dev leftovers.
- Spot “Deep Pages”—anything more than 3-4 clicks from the homepage is at risk of being ignored by crawlers.
How to fix: - Add internal links from high-traffic or relevant pages. - Update navigation, or use related articles/products widgets.
6. Assess Crawl Budget Waste
Enterprise sites are notorious for wasting crawl budget on junk:
- Endless filtered/faceted URLs
- Session IDs or tracking parameters in URLs
- Staging/dev environments accidentally indexed
Use SEMrush’s “Crawled Pages” and “Parameters” reports to spot these. If you see thousands of URLs with “?sort=” or “?sessionid=”, you’ve got a problem.
What to do: - Block junk URLs in robots.txt - Use canonical tags wisely - Add URL parameter rules in Google Search Console
7. Review Core Web Vitals (But Don’t Panic)
SEMrush shows basic Core Web Vitals data, but it’s no substitute for Google Search Console or PageSpeed Insights. Use it for a high-level scan, not deep analysis.
- Look for patterns—if whole sections of your site are slow, it’s usually a templating or infrastructure problem.
- Don’t chase every low score—focus on templates and pages that drive traffic.
Honest take: If your dev team is already tracking CWV in their own tools, SEMrush’s reports are a “nice to have,” not a must.
8. Export & Share Actionable Reports
SEMrush loves dashboards, but execs and dev teams don’t want to log in. Export what matters:
- CSV/Excel exports for developers (broken links, duplicate URLs, orphaned pages)
- PDF summaries for leadership (“Here’s 3 things breaking our SEO—let’s fix them”)
- Custom filters—don’t just dump 10,000 errors on someone’s desk. Slice by priority, section, or template.
Pro Tip: Add clear context when sharing. “This issue affects 12,000 product pages and could waste crawl budget” beats a generic “errors found” message.
9. Create a Fix List and Track Progress
A giant to-do list is useless. Triage what’s urgent, what’s easy, and what’s “nice to have.”
- Fix critical blockers first: Broken links, robots.txt disasters, huge duplicate content.
- Batch fixes by template or section: Don’t try to fix 1,000 pages one by one.
- Re-crawl after big changes: SEMrush makes this easy—run another audit, compare results.
What not to do: Don’t obsess over 100% “clean” audits. Big sites are never perfect, and that’s fine.
10. Keep It Simple—Iterate As You Go
Technical SEO for enterprise sites is never “done.” Sitemaps change, devs break things, priorities shift. The key is to set a regular audit cadence—monthly or quarterly is usually plenty.
- Document what you fix and why.
- Automate alerts for new critical issues.
- Don’t get lost in the weeds—focus on what moves the needle.
Big sites are complicated, but your audit process shouldn’t be. Use SEMrush for what it does well: finding big, structural issues fast. Ignore the noise, fix what matters, and keep moving. You won’t get everything perfect, and that’s normal. The most effective SEOs are the ones who keep it simple and just keep going.