Most SEO audits are just checklists: they check boxes, list vague “issues,” and fail to connect the dots between what’s broken and what affects performance. Best SEO agencies take a different approach: they conduct SEO audits to diagnose business-impacting problems.
Here’s what separates the Best SEO agencies from those who only use template-based reports.
1. Deep Dive Crawl: Beyond Broken Links
Leading agencies begin with a site-wide crawl using tools like Screaming Frog, Sitebulb, or JetOctopus to conduct site-wide crawl.The goal isn’t just to find broken links but to also understand how Googlebot is crawling the site, what’s being ignored, and where crawl budget is wasted.
For large sites (over 10,000 URLs), this becomes critical. Crawl logs often reveal that a significant portion of Googlebot crawl requests hit faceted navigation pages blocked by robots.txt, which is a textbook example of crawl budget misallocation. Many of these often do not show up in many SEO audits.
What to check:
- Percentage of pages indexable vs total URLs
- Depth from homepage (ideally keep core content within 3 clicks)
- Orphan pages with backlinks
- Canonical discrepancies
- Parameterized URLs without proper handling
2. Tech Fixes: Prioritize for Profit
Once an audit is done and all the technical “errors” are discovered, best SEO prioritize fixes. Experienced SEO agencies triage issues using their proven methods which may be based on severity and visibility. For example, a page generating 30% organic traffic which has a broken canonical matters more than a page with low traffic that has a missing alt attribute.
Agencies typically use a weighted scoring system that blends:
- Estimated traffic value (via Google Search Console and GA4)
- Depth and crawl frequency
- Backlink equity per page (via Ahrefs or Majestic)
- Indexation status over time (using log analysis)
This allows them to show clients where technical SEO fixes will actually improve rankings or preserve performance, not just “clean up” the site.
3. On-Page SEO: Intent Over Keywords
Ideally, an SEO audit should not focus only on word count or how many times a targeted keyword shows up. Best SEO agencies review what’s actually ranking. They spend time examining the top 10 results for a targeted search, review each page’s structure, and identify what is working in terms of answering the searcher’s intent.
If a website’s product page is trying to rank for a query where Google shows mostly category roundups or comparison guides, then no amount of tweaking headers will help. Content type mismatch is one of the most common issues uncovered and often the reason high-quality pages underperform.
Smart audits include:
- SERP content type analysis (informational vs transactional)
- Structured data validation (with tools like Google’s Rich Results Test)
- Word-to-code ratio checks for bloat
- Accessibility and load speed benchmarks (via WebPageTest and Lighthouse)
4. Analytics Audit: Trust Your Data
Incorrectly set up or misconfigured analytics wrecks SEO efforts. This is why best SEO agencies include validating tracking accuracy in their audits. They compare Google Analytics (GA4) data against server logs and Search Console data to spot inconsistencies such as session inflation due to duplicate tags. Some pages may be missing key call to action (CTAs) resulting in underreported conversions.
Best SEO agencies also check for:
- GA4 tag health (ideally implemented via Google Tag Manager)
- Cross-domain tracking setup
- Source/medium discrepancies in landing pages
- Conversion path mapping in relation to organic sessions
This step ensures that any SEO performance improvements later are based on reliable data, not guesswork.
5. Content Inventory: Find Your Gold (and Trash)
Leading audits don’t stop at the crawl. They run a full content inventory using tools like Screaming Frog, Google Search Console, and historical GA4 or Looker Studio dashboards. Then they track decay trends.
Content decay, especially common with blogs, is when content on websites slowly stops performing well and being seen. Over time, some content that used to do well might start getting fewer than 10 clicks a month, for example. That usually happens when the page doesn’t cover the topic well enough, has outdated information, broken internal links, or simply just covers the same as other pages on the site, making it redundant. In these cases, rewriting or re-optimizing content can help regain lost rankings.
Standard process:
- Export URLs with organic traffic <10 visits/month
- Look for keyword cannibalization using Ahrefs or Semrush
- Prioritize pages with backlinks or historic rankings for updates
- Mark content with zero backlinks, no rankings, and poor engagement for removal or consolidation
6. Local SEO: Dominate the Neighborhood
For businesses with physical locations, local SEO is its own audit layer. Verified agencies will dig into:
- NAP (Name, Address, Phone) consistency across the top directories (using tools like Whitespark or BrightLocal)
- Google Business Profile optimization (category usage, Q&A, photos, review recency)
- Local landing page indexation and internal linking
- Proximity signals and map pack ranking gaps
Even small inconsistencies like mismatched hours across aggregator sites can cause suspensions or drops in visibility. In many audits, these types of issues are flagged early and resolved before they cause broader search visibility problems.
For international or multilingual sites, the audit includes hreflang audits (manual and automated), URL structure validation, and language-based crawl tests. ccTLD vs subfolder vs subdomain strategies are reviewed based on the site’s expansion plans.
7. SEO Action Plan: Results, Not Reports
The best audits don’t end with findings but with implementation blueprints. Agencies break recommendations down by:
- Department (dev, content, UX, analytics)
- Timeline (what can be fixed in 30 days vs 90+)
- Technical complexity (some fixes require no code changes, others need sprint planning)
- Estimated outcome (traffic increase, crawl efficiency, conversion lift)
Instead of saying “fix 404 errors,” the final doc might say: “Redirect these 31 expired product URLs with backlinks to new equivalents. Estimated recovery: 2,300 lost monthly visits and 18 referring domains.”
Clients know exactly what to do, who should do it, and why it matters.
How to Get This Kind of Audit
Most audits don’t look like this as they’re often too shallow, too automated, or disconnected from business outcomes. But some agencies do it right because it’s the only way to build SEO strategies that work in 2025’s search environment.
Want to find teams that audit this way? Check out our list of verified SEO agencies. Every agency listed has been vetted for real-world results, not just pretty decks.