SEO audit tools: which one to use at each phase

By Miguel Ángel Jiménez, Head of SEO at Gecko Studio

There are hundreds of lists out there with "the best SEO tools". They all share the same problem: they tell you what exists, but not when to use it. The usual outcome is that you have four or five tools installed, you don't know where to start, and you end up using only Search Console "because at least you understand it".

This article works differently. It organises tools by phase of a real SEO audit — the same phases we follow at Gecko Studio when we audit a site — and explains exactly when each one comes in and what specific data it contributes. The order matters: you don't analyse on-page before knowing whether Google can index the pages, just as you don't optimise content before confirming the site loads correctly on mobile.

If you don't yet have a clear picture of the full process, the starting point is the step-by-step SEO audit guide, where we explain each block in detail. Here we focus on the toolkit: which tool at which moment and, above all, which is free and when it makes sense to pay.

Why the order of tools changes the results

An SEO audit is not a 200-item checklist you can review in any order. It is a structured process in blocks where the diagnosis of each one conditions the interpretation of the next. Starting with on-page without having checked indexation can lead you to spend hours optimising pages that Google has already decided to ignore. Reviewing the link profile before having a clean technical foundation is building on cracked ground.

Mixing tools without a sequence produces misleading conclusions. For example, Screaming Frog can detect that 30 % of your pages have a duplicate meta description — a real technical finding — but if you haven't first looked at Search Console to see how many of those pages are actually indexed, you may be optimising pages with zero organic visibility. The right tool at the right moment. That is the difference between an audit that improves rankings and a report that gets filed away.

Phase 1 — Indexation and crawling: is Google reaching your content?

Everything starts here. If Google cannot crawl and index a page, no other improvement will have any effect. The first question of any audit is: does Google know what exists on this site, and does it have access to it?

Google Search Console is the central tool in this phase and is completely free. The Page Indexing report — previously called Coverage — shows how many URLs are indexed, how many are excluded, and the exact reason for each exclusion. The Sitemaps report confirms that the site map is registered and that Google processes it without errors. The URL Inspection report lets you check, one by one, whether a specific page is in the index and how Googlebot last saw it.

Screaming Frog SEO Spider covers what GSC cannot cover by definition: crawling from the perspective of an external bot. Its free version crawls up to 500 URLs and detects blocks in robots.txt, pages with noindex, chained or looping redirects, and 404 error pages that still receive internal links. The combination of GSC (what Google sees) and Screaming Frog (how the site is structured) gives the complete picture of indexability.

Bing Webmaster Tools plays the same crawl-diagnosis role for Bing. Many projects ignore it, but in B2B sectors and some European markets, Bing can account for 10 to 20 % of organic traffic. It is free and takes minutes to set up. In the audit, the aim is to verify there are no Bing-specific coverage blocks or issues that go unnoticed when looking only at GSC.

What is analysed in this phase:

• Indexed pages vs. total pages on the site: is there a significant gap?
• Reason for exclusions: noindex, blocked by robots.txt, "discovered but not crawled", "crawled but not indexed".
• Sitemap status: processing errors, URLs returning a status other than 200.
• Chained redirects and redirect loops that drain the crawl budget.

Phase 2 — Technical performance: does it load fast and work on mobile?

Once it is confirmed that Google can access the content, the next block is technical performance. The reference metric since 2021 is Core Web Vitals: LCP (loading time of the main content), INP (response to interactions) and CLS (visual stability of the layout). They are confirmed Google ranking signals and, above all, they reflect the real user experience.

PageSpeed Insights is Google's free tool for measuring these values. It combines field data — real measurements from Chrome User Experience Report (CrUX) users — with simulated lab data. It analyses both the mobile and desktop versions and provides specific technical recommendations with an estimated performance impact, prioritised from highest to lowest. It works URL by URL, making it ideal for analysing the most critical pages on the site.

Google Lighthouse is integrated directly into Chrome (F12 → Lighthouse tab) with no additional installation. It runs performance, accessibility, basic SEO and best-practices analyses on any URL, including pages behind a login or in a staging environment. The key difference from PageSpeed Insights is that Lighthouse simulates controlled lab conditions, making it the diagnostic tool: when PageSpeed Insights detects a problem, Lighthouse helps identify the exact technical cause.

In practice, the two are used together: PageSpeed Insights to understand the real state in production; Lighthouse to diagnose what is causing it and to test the impact of changes in staging before applying them.

Search Console also includes an aggregate Core Web Vitals report grouped by page type — categories, product listings, posts — which makes it possible to spot patterns: for example, that all category pages have a slow LCP while individual product pages are in the green. That finding guides where to concentrate the technical work.

What is analysed in this phase:

• LCP, INP and CLS on mobile (priority) and desktop.
• Render-blocking resources (JavaScript and CSS in the critical path).
• Images without defined dimensions that cause layout shifts (CLS).
• Third-party fonts loaded synchronously, external CDNs that add latency.
• Full HTTPS status: no mixed content, no unnecessary HTTP-to-HTTPS redirects.

Phase 3 — On-page SEO: is each page properly optimised?

This is where the most time is spent on medium and large sites, and where a mass-crawl tool makes a real difference compared to a manual analysis that would take weeks.

Screaming Frog SEO Spider is also the reference tool in this phase. The free version (up to 500 URLs) extracts in a single pass: titles, meta descriptions, H1s, H2s, HTTP response codes, canonicals, hreflang, image alt attributes, crawl depth, orphan pages with no internal links pointing to them, redirects, and more. For sites of up to 500 URLs — small businesses, microsites, local service sites — it covers the complete on-page audit. For larger sites, it allows you to select the most critical sections within the limit.

One limitation to bear in mind: free Screaming Frog does not render JavaScript natively. For sites built with React, Next.js or Angular where content is loaded client-side, the on-page data it extracts may be incomplete. In those cases the crawl needs to be supplemented with Lighthouse analysis or GSC URL Inspection for representative pages.

Google Search Console adds the layer of real performance data on top of on-page: CTR, impressions and average position for each URL. Crossing Screaming Frog's structural data (the page has a 38-character title and the correct H1) with GSC data (that page has a 1.2 % CTR on 8,000 impressions) is the most powerful combination for prioritising what to optimise first.

What is analysed in this phase:

• Missing, too-short, too-long or duplicate titles across pages.
• Missing or duplicate meta descriptions.
• Multiple H1s on the same page, missing H1s, or H1s that do not contain the page's target keyword.
• Incorrect canonicals or canonicals pointing to error URLs.
• Incorrectly implemented hreflang on multilingual sites (for detail, see the international SEO audit guide).
• Images with no alt attribute or a generic alt.
• Orphan pages with no internal link pointing to them.

Phase 4 — Content and relevance: does your content answer what users are searching for?

On-page confirms that the technical elements are in order. The content block answers a different question: is the content on each page aligned with the intent of the user arriving from organic search?

Google Search Console remains the central tool. The Search Performance report shows exactly which queries trigger each URL, with how many impressions, how many clicks, and at what average position. That data enables three critical diagnoses. First, detecting cannibalisation: when two URLs on the same domain compete for the same primary query, GSC reveals it because both show impressions for that term. Second, identifying quick wins: pages ranking in positions 8–15 with solid impressions that need a content improvement to break into the first page. Third, detecting low CTR issues: if a page has many impressions but a low click rate for its average position, it is likely that the title or meta description is not communicating the page's value effectively.

Google Analytics 4 (GA4) adds the post-click behaviour layer: bounce rate, session duration, pages per session, conversion events. A page receiving organic traffic but with a very high exit rate can indicate a mismatch between user intent (what they expected to find when clicking) and the actual content on the page. GA4 is not an SEO audit tool in the strict sense, but it closes the loop: GSC tells you how much traffic arrives, GA4 tells you what that traffic does once it lands.

Bing Webmaster Tools includes its own keyword report and an analysis of pages with thin content according to its crawling criteria, which can flag thin content that GSC does not mark explicitly.

For keyword research beyond what you already rank for — search volumes, difficulty, competitor opportunities — Google's native options (Keyword Planner, available with a Google Ads account even without an active campaign) provide orientation, but more precise and complete data requires paid tools. Ahrefs, Semrush or SE Ranking are the industry benchmarks for this type of analysis. It is not possible to give exact limits or pricing here as these change frequently, but any entry-level plan gives access to volume and competition data significantly more reliable than free estimates.

What is analysed in this phase:

• Queries with many impressions but average position >10 (untapped potential).
• CTR below the expected benchmark for each position.
• Cannibalisation between pages competing for the same intent.
• Pages with no organic traffic after six or more months of indexation (thin content, unresolved intent, or no real demand).
• Outdated content with stale dates, data or references that damage credibility.

Phase 5 — Structured data: does Google understand what type of content this is?

Structured data — Schema.org markup in JSON-LD format — tells Google precisely what type of entity each page represents: an article, a product, a FAQ, an event, a recipe, an organisation. When implemented correctly, they can produce rich results in the SERP: star ratings, expandable FAQ lists, product cards, event schedules. They are not a guarantee of a rich snippet, but they are a necessary condition for being eligible for one.

The official tool for verifying them is Google's Rich Results Test (available at search.google.com/test/rich-results). It analyses a URL or a code snippet and confirms which types of structured data it detects, whether they are technically valid, and whether they are eligible to appear as a rich result. It is free with no per-URL usage limit.

For validating Schema.org markup in a generic way — outside the Google ecosystem, or for schema types that Google does not yet process — the official Schema.org Validator (validator.schema.org) is the technical reference. Also free.

Search Console includes a "Search appearance" section showing the status of all structured data detected across the site: types found, syntax errors, missing required properties, and warnings. That is the continuous monitoring dashboard; the Rich Results Test is the per-URL diagnostic tool.

What is analysed in this phase:

• Which Schema types are implemented and which should be implemented given the content type.
• Syntax errors in the JSON-LD markup (incorrectly formatted properties, unrecognised types).
• Missing required properties that prevent eligibility for rich results.
• Inconsistencies between what the markup states and the content visible on the page (Google may take action if a discrepancy is detected).

Phase 6 — Link profile: who links to your site and with what authority?

This is the only phase where free tools show structural limitations. Google Search Console includes a "Links" report showing the external domains that link most, the most-linked pages, and the most frequent anchor texts. It is a useful starting point, but the backlink index that Google exposes in GSC is partial: it does not reflect all the links it crawls, nor the relative authority data of the referring domains.

For a complete link profile analysis — detecting an anchor profile with excessive concentration in branded or money-keyword terms, measuring domain authority relative to competitors, identifying recoverable broken backlinks, or finding link-building opportunities — paid tools are required. Ahrefs (Site Explorer), Semrush (Backlink Analytics) or SE Ranking are the industry benchmarks. The difference between the data they show and GSC data is particularly significant on sites with complex link profiles or in sectors where link building is a meaningful ranking factor.

The technical SEO audit we carry out at Gecko Studio includes a full link profile analysis with complete data, including referring domains, anchor distribution and recoverable broken backlinks. For projects where links are a critical factor, this phase does not admit the shortcuts that the earlier ones allow.

What is analysed in this phase:

• Number of unique referring domains and their relative authority (Domain Rating or equivalent).
• Anchor text distribution: balance between brand, bare URL, keyword and generic anchors.
• Pages on the site receiving the most external links (do they coincide with the strategically most important ones?).
• Broken backlinks: inbound links pointing to URLs returning 404 that could be recovered with a redirect.
• Referring domain profile over time: organic growth or anomalous spikes.

Infographic: recommended tool by phase (with free availability)

The following table contains the complete matrix of phases, tools and availability. The infographic shows the same data visually.

Text equivalent — the same data as the infographic:

Where to start if you have never audited your site before

If you are starting from scratch and want an initial picture before opening any tool, the fastest route is an automated analysis covering the most critical points. At Gecko Studio we offer a free SEO analysis that reviews the main blocks of any site in seconds: indexation status, loading speed, basic technical errors, and a prioritisation of the most urgent issues. It is the recommended entry point before spending hours installing and configuring tools individually.

Once you have that initial diagnosis, you know which phases have the most work ahead and can concentrate the detailed analysis — with the tools described above — where it will have the most impact. There is no point investing hours in content analysis on a site that has unresolved critical indexation issues.

If you want to understand the full structure of the process before executing it, the step-by-step SEO audit guide covers every block in detail with examples. And if you are looking for the structure with a real completed case, the SEO audit template shows exactly what this work looks like done properly with data from a real project.

When it makes sense to invest in paid tools

Free tools cover the audit of your own site well when the aim is to diagnose technical, indexation, on-page and structured data issues. The limitations appear in three specific situations where the move to paid tools is justified:

Competitor analysis. To understand why a competitor ranks where you don't — how many referring domains they have, with what anchors, which pages receive the most links — the data you need is external to your site. Search Console only gives you data about your own domain. Tools such as Ahrefs, Semrush or SE Ranking have their own backlink and estimated traffic indices that make it possible to analyse any domain, whether your own or a competitor's.

Scale. Free Screaming Frog falls short on sites with more than 500 URLs. For an e-commerce site with thousands of product pages, a content portal with hundreds of categories, or any site with a deep architecture, the paid version removes that limit. It also unlocks additional features such as JavaScript-rendered crawling, direct integration with GA4 and GSC to cross-reference data inside the tool, and comparative analysis between crawls to detect changes across audits.

Keyword research. When the goal is not just to diagnose what you already rank for, but to find opportunities you are not yet exploiting — search volumes, ranking difficulty, SERP analysis for a target keyword — paid tools provide data that is significantly more complete and reliable than Google Keyword Planner.

For a complete professional audit as we run at Gecko Studio, we use the free toolkit as the foundation and add Ahrefs as the data layer for backlinks, keywords and competition. If you want to see what that process looks like applied to your site, you can find the detail on the SEO audit service page.

Frequently asked questions about SEO audit tools

Can you run a complete SEO audit without paying anything?

Yes, with caveats. Google Search Console, Screaming Frog up to 500 URLs, PageSpeed Insights, Lighthouse, GA4 and the Rich Results Test cover the indexation, technical performance, on-page and structured data phases. The area where free tools fall short is the backlink profile analysis and keyword research beyond what you already rank for. For those two areas, paid tools (Ahrefs, Semrush, SE Ranking) are practically necessary if you want rigorous data.

What is the difference between PageSpeed Insights and Google Lighthouse?

PageSpeed Insights shows real user data from the Chrome User Experience Report (CrUX) when sufficient data is available for the site, alongside a lab simulation. Lighthouse simulates controlled conditions only. In practice: PageSpeed Insights tells you how real users experience the page; Lighthouse helps you diagnose the technical cause. Use both: first PageSpeed Insights to understand the real state, then Lighthouse to identify what is causing it and to test the impact of changes before applying them.

Is free Screaming Frog enough for a serious audit?

For sites of up to 500 URLs, yes. The free version extracts all relevant on-page data — titles, meta descriptions, H1s, canonicals, hreflang, HTTP codes, images without alt, broken internal links — and is sufficient to audit the bulk of on-page issues for a small business or service site. On larger sites you need to decide which sections to prioritise within that limit, or invest in the paid version which removes the limit and adds additional features.

Do I need Google Analytics 4 for an SEO audit?

It is not essential for the technical and on-page sections, but it is very useful in the content block. GSC tells you how much organic traffic reaches each page; GA4 tells you what that traffic does once it lands: whether it bounces immediately, whether it navigates to more pages, whether it converts. That information is key to detecting pages with traffic but with content that does not resolve the user's intent. If you don't have GA4 installed, set it up before starting the audit so you have data available at the time of the diagnosis.

Why doesn't Ahrefs or Semrush appear in the free phases?

Because their most valuable functions for an audit — complete backlink analysis, competitor keyword data, estimated traffic for third-party domains — require a paid subscription. Both have free trial versions or limited free tiers, but with significant restrictions that make them of little use for systematic analysis. In this article they are recommended for the phases where the data they provide has no real free substitute: link profile analysis and keyword research beyond your own domain.

Which tool should I use if I can only use one?

Google Search Console. It is free, has no URL limit, and provides data across five of the six audit phases: indexation, technical performance (CWV), on-page (performance by URL), content (queries, CTR, cannibalisation), and a basic link profile. If you can only configure and review one tool, it is the one that delivers the most diagnostic value for the lowest setup cost.

When should I hire a professional SEO audit instead of doing it myself?

When the site has more than 1,000 URLs, there are versions in multiple languages, traffic has been falling for months without a clear cause, or a migration has just been completed. In those cases, the complexity of cross-referencing data from several tools and prioritising correctly goes beyond what free tools allow you to diagnose independently. The SEO audit service at Gecko Studio is designed for these scenarios: complete diagnosis with real data, prioritised actions and an executable roadmap.

SEO audit tools are the means, not the goal

The most common mistake when discussing SEO tools is treating them as the object of the audit. Tools produce data; the audit is the process of interpreting that data, identifying the issues with the greatest impact on rankings, and turning them into a concrete action plan. A Screaming Frog report with 400 unprioritised issues is worth less than a diagnosis of 20 problems ordered by real impact.

The phase framework in this article is not arbitrary: it is the order in which each diagnosis makes sense given what has been verified before. Indexation first, because without it nothing else matters. Technical next, because a slow-loading site loses traffic regardless of how well the on-page is set up. Content and links last, because they are the most costly layers to improve and deserve attention only once the technical foundation is sound.

If you want to apply this process to your own site and don't know where to begin, the first step is to get a picture of the current state. Our free SEO analysis gives you that initial picture in seconds, with no registration required: indexation, performance and basic on-page, with the priority issues identified. From there you know which phases to concentrate the detailed analysis on, using the tools described above.