How to Do an Enterprise SEO Audit the Right Way

If you’re in charge of driving qualified organic traffic and sales for a large, enterprise-level website, you’ve probably realised by now that a basic SEO checklist just won’t cut it. What you really need is a strategic framework; one that’s tailored to your client’s unique challenges, while simultaneously making a compelling case to key stakeholders that your approach is the smartest path to improving the bottom line.

Over the years, working as an enterprise SEO consultant, I’ve developed a system that digs much deeper than surface-level audits CMOs are so used to seeing. It’s built to uncover meaningful insights that actually move the needle (whether you’re working with one thousand pages or one million).

While the problems and solutions are custom-tailored to the website in question, the core processes stay the same: find the gaps, prioritise by business impact, and build a roadmap that secures buy-in and drives results.

In this post, I’ll walk you through my step-by-step process for creating an advanced enterprise SEO audit, designed to reveal hidden opportunities, reduce internal friction, and fuel long-term growth.

Let’s dive into this process’s first (and arguably most critical) step.

This article is a guest contribution from Mark Howser, Enterprise SEO Consultant at Digital Snowstorm.

Start with a Technical SEO Audit

When you’re managing millions of pages, you already know that Enterprise SEO hinges on a rock-solid technical foundation. At this scale, even minor development missteps can cause site-wide issues that quietly throttle organic performance.

That’s why we always begin with a technical audit; it reveals the subtle yet high-impact opportunities that drive scalable growth, while simultaneously giving you a deeper understanding of the complex Information Architecture (IA) you’re about to tame in the content and link audits.

Tools I Use

• Screaming Frog SEO Spider: Crawling data, API integrations, custom search/extraction
• Google Analytics 4: Performance insights
• Google Search Console: Performance and indexing insights
• Manual spot checks: Catch what tools might miss

What to Look For

For each issue you uncover, include a brief, layman-friendly description of what the issue is and why it matters, along with a high-level recommendation for resolution in a Google Doc. The proposed solution doesn’t need to be overly detailed; it just needs to be a rough outline of how you plan to approach the issue in the coming months (so that the client begins to build confidence in their decision to hire you).

Group items into these three categories:

1. Site Crawling & Indexing
2. Site Structure & Navigation
3. Page Speed & Mobile UX

Bonus: You could add a 4th section called ‘Site Management’ where you outline issues with their GTM and GA4 deployment. Even though it doesn’t really fall under ‘Technical SEO,’ having a clean and accurate performance tracking solution is critical for proving your worth to the client, and you should always prioritise setting this up correctly before you begin a campaign.

Once you have all of the issues documented, assign a priority (P1–P4) to each item based on potential business impact, and reorganise each task by priority level. If you’d like to also denote the primary teams that will be involved in resolving the issue, you can do so throughout the tech/content/link audits (like the example above).

Audit Content by Performance & Intent

Once you have a clear understanding of the site’s technical framework, it’s time to audit content performance by page type.

My Process

• Use the Screaming Frog SEO Spider’s API connectors to pull data from Ahrefs, Google Search Console, and GA4.
  • Filter GSC data (using regex) to isolate non-branded traffic, and filter GA4 data to isolate organic traffic (within the API integration configs).
• Add a new column to the Screaming Frog SEO Spider export to manually categorise URLs into page groups (e.g., product categories, product detail pages, location pages, blog posts, etc.).
• Create bar charts (within Google Sheets) showing performance for each page group with the following insights: total keywords vs top 10 keywords, non-branded clicks vs non-branded impressions, signups/sales, new users vs total users, etc.
  • Add these bar charts to your ‘Content Audit’ Google Doc, and provide detailed explanations of what you’re seeing in this data.

Then manually review (and report on) a few top-performing and underperforming pages for each page group using the criteria below:

• AIO (AI Optimisation & Featured Snippets Readiness)
  • Is the content structured with clear questions and concise answers?
  • Are key facts/numbers/data highlighted in formats AI prefers (e.g., tables, bullet points, bolded statements)?
  • Is the page using conversational formatting and other AI-friendly elements (e.g. FAQs, HowTo’s, etc.) to increase AI visibility?
• E-E-A-T (Experience, Expertise, Authoritativeness, Trustworthiness)
  • Is the content written by a subject matter expert (or clearly shows real experience)?
  • Does it cite reputable sources or include original data/insights?
  • Is the author bio present and trustworthy?
  • Is the content useful and unique?
• Keyword Targeting & Semantic Coverage
  • Are primary and secondary keywords naturally integrated into title tags, H1s, subheaders, and body text?
  • Is the content covering semantically related entities/topics?
  • Does the page structure and content align with user intent?
• Conversion Flow & UX Alignment
  • Do CTAs align with the intent of the page and the current stage of the user journey?
  • Is the layout skimmable and engaging (e.g., clear subheadings, bullets, concise paragraphs)?
  • Is multimedia used to enhance the user experience (videos, images, AI text readers, etc.)?

This stage will help you reveal high-potential, low-performing groups to prioritise (after you’ve optimised high-intent pages), along with specific strategies like re-optimising existing content, eliminating and redirecting low-quality content, improving page designs or CTAs for CRO purposes, and much more.

Evaluate Link Equity Distribution

Regardless of what some might say, backlinks still matter (especially in highly competitive verticals). In fact, a study by Ahrefs found that 96.55% of pages on the internet receive no organic traffic whatsoever, one of the key differentiators for the top 3.45% being that they had a high-quality backlink portfolio.

Understanding the flow of both internal and external link equity will help you ensure that you’re harnessing the full potential of every link.

Steps to Follow

1. Use the Ahrefs API in the Screaming Frog SEO Spider to pull backlink data, and reuse the page groups you laid out earlier.
2. Layer in the number of internal links flowing to each page (see “Link score” and “Unique inlinks” in the SEO Spider report, or reference the Links → Internal links report in Search Console) to identify the flow of your internal link equity for each page group.
3. Manually audit the quality of internal links flowing to your ‘money pages’
   1. Check their anchor text, if they’re coming from nav links vs body content, if they’re coming from high UR pages, etc. (Screaming Frog SEO Spider → Bulk Export → Links → All Anchor Text).
4. Using the page groups and Ahrefs API data, analyse the external link equity flowing to your various page groups across:
   1. Domain/URL Rating
   2. Follow vs NoFollow links
   3. Backlinks vs Referring Domains
5. Using Ahrefs’ Overview data (within the Ahrefs platform itself, not the SEO Spider/API), compare backlink metrics with competitors (and generate bar charts):
   1. Domain/URL Rating
   2. Follow vs. NoFollow links
   3. Referring Domain Rating distribution
   4. Etc.

What to Uncover

1. Which pages and page groups have the strongest internal and external link equity?
2. Where can you optimise the flow of the internal and external link equity?
3. How does your link profile stack up against competitors?

Use these insights to justify launching or expanding link-building campaigns to the stakeholders, and lay out some strategies that would be useful to their particular situation, such as:

• Run digital PR campaigns tied to product launches, proprietary research, or industry awards to earn high-authority media coverage and backlinks.
• Create linkable assets like calculators, research studies, data visualisations, or free tools that solve specific problems.
• Use the Skyscraper Technique by finding top-performing content in your niche, creating something demonstrably better, then promoting it to those who linked to the original piece.
• Build an affiliate program to attract natural links from partners promoting your products or services.
  • Be sure to have your affiliates use rel="sponsored" links when they link to your site (to mitigate the potential for a negative reaction from Google). Even though these links don’t pass link equity, they can help build positive brand sentiment, which can help SEO performance in less direct ways.
• Develop a thought leadership program by empowering C-suite or subject matter experts to contribute content, speak on podcasts, or participate in panels.
• Guest post on niche-relevant, high-authority blogs and industry publications to build backlinks and credibility.
• Host expert roundups, interviews, or surveys and notify participants of the results (to encourage backlinks and social sharing).
• Invite influencers or well-known contributors to write for your blog to earn links from their audiences and boost trust.
• Reclaim unlinked brand mentions by requesting attribution.
• Fix broken backlinks by identifying and recreating lapsed or outdated content others previously linked to.
• Repurpose high-performing content into visuals like infographics or charts to attract links from publishers that prefer embeddable assets.
• Use LinkedIn Sales Navigator, Ahrefs’ Content Explorer, manual research, and outreach tools (like Apollo.io or Pitchbox) to identify and pitch editors, writers, and content leads in your niche (ideally leveraging the assets previously mentioned).
  • Just make sure your top priority is to help them, rather than asking them to do something for you. And be willing to offer $100 Amazon gift cards or $250-500 for their services in follow-up sequences if your first message gets ignored (it likely will since these people get spammed every day).
• Etc.

Build a Keyword-Driven Content Strategy

With audit insights in hand, it’s time to build a content roadmap informed by real demand (not assumptions).

How I Build the Strategy

1. Run a content gap analysis in Ahrefs to find non-branded keyword opportunities.
   1. Include the keywords your client’s domain ranks for in the analysis, along with 5–10 of their top organic competitors.
2. Manually review thousands of keywords and highlight ones that are relevant to the business (include top, middle, and bottom of funnel terms).
3. Extract seed terms (use ChatGPT, a word cloud, or manual review to isolate seed terms).
   1. Merge these with insights from your onboarding survey to create a full seed list.
4. Plug your seed terms/word combinations into Ahrefs’ Keyword Explorer to find related terms.
   1. Use filters as you see fit (e.g., KD < 70, SV > 100, includes ‘football’, excludes ‘basketball’).
5. Export your list and remove any irrelevant keywords that may have slipped through.
6. Cluster keywords with Keyword Insights (Settings: 4 matching pages, agglomerative).
   1. Manually refine the Keyword Insights output by combining or breaking out keyword groups as you see fit, and eliminating some as needed. Sometimes Keyword Insights breaks them out into too many groups or combines informational with transactional due to a bad Google SERP combination.
7. Use Excel formulas like this one to recalculate the total volume for each keyword grouping after you’ve cleaned the sheet:
   =SUMPRODUCT(SUMIF('Keyword Volumes'!A:A, 'Keyword Groupings'!$D2:$L2, 'Keyword Volumes'!C:C))
   1. ChatGPT can help you adapt this formula to your specific needs, but in the example above, Column A is the keyword, and Column C is the Search Volume.
8. Layer in new columns (and provide GPT for Sheets with specific rules to automate this work):
   1. Recommended page type (blog, service, page, text, etc.) based on the primary keyword’s search intent.
   2. A clickworthy title to consider using based on the primary keyword’s search intent and page type.
   3. Level of importance to the business.
   4. The URLs for existing pages you could optimise around a keyword grouping (you’ll be able to use the Keyword Insights export that shows URLs for each keyword to match this up appropriately using a VLOOKUP).

Once you’ve done that (and you’ve consolidated the content roadmap even more to reduce redundancies), you’ll be in a position to forecast traffic and conversion potential for each page group. And by breaking it out for each page group, you’ll be able to adjust the conversion rates according to GA4 data (since blog posts won’t convert at the same rate as your high-intent pages will).

So in this next step, you’ll lay out traffic and conversion estimates for each page group, assuming you were ranking in positions 1, 5, and 10 for all of the keywords in that page group. This isn’t intended to be a perfect forecast; just good enough to get buy-in from key stakeholders and to help you prioritise your efforts according to potential impact.

Now that you’ve uncovered powerful insights and future opportunities, here’s where the real magic happens: turning them into a clear, actionable roadmap that key stakeholders can rally behind.

Create a 12-Month SEO Roadmap

In this final step, the primary purpose is to tie everything together into a clear, strategic roadmap that’s fully aligned with the underlying business goals.

Roadmap Framework

Create 4-5 strategic pillars that will resonate with the client, such as:

• Expand Audience Reach (new and optimised content)
• Maximise Conversions (CRO, UX/UI improvements)
• Increase Authority (link building, digital PR)
• Strengthen Technical Framework (indexation, speed)
• Strategic Advice & Support (reporting, client communication, planning, etc.)

And place each SEO task into one of those buckets. What you’re doing here is helping the client visualise how individual tasks tie back to key pillars, and how the key pillars tie back to the overall business goals (improve LTV:CAC, improve marketing budget efficiency, increase revenue, etc.).

Next, lay out when you’ll tackle each task over the next twelve months (or longer if the client’s budget doesn’t permit its completion in that timeframe). Use rows for each task, columns for the intended months you’ll work on a particular task, and in each corresponding cell, use checkmarks for scheduling. Include two additional columns:

• Estimated hours for each task (per month if expanded over a multi-month timeframe)
• Hourly rate x hours = cost

And use this formula (you can have ChatGPT adapt it to your specific sheet) in a row below the table to calculate the total cost of all tasks worked on for a given month to see how close to the client’s monthly budget you are:

=SUM(ARRAYFORMULA({Hours * Rate Column} * ({Checkmark Column for a Given Month} = TRUE)))

By running these time/cost calculations, you’ll be able to plan out your client load months in advance, work ahead to be well-positioned for time out of office, ensure that your plan is within the scope of the client’s budget, and minimise potential scope creep.

Final Thoughts

As you can see, Enterprise SEO isn’t just about identifying issues and fixing them; it requires you to earn buy-in from the people who set the SEO budget. To do that, you need more than a list of tasks; you need a strategic plan that speaks their language. That means telling a compelling story and clearly quantifying the business impact of your strategy.

When you combine technical expertise, deep performance insights, and a little bit of financial acumen, your audit transforms from a dismissible checklist into a compelling map to find the hidden treasure buried within the website.

That said, this kind of deep-dive audit does take time, and it can be overkill for some clients (e.g., a 2,000-page website doesn’t need this much depth; you could likely do the audits without documenting your findings and just focus on building the SEO roadmap).

Here’s a rough estimate of how long each part typically takes me:

• Technical Audit: ~10 hours
• Content Audit: ~5-10 hours
• Link Audit: ~5 hours
• Content Roadmap + Forecasting: ~25 hours
• 12-Month SEO Roadmap: ~2-3 hours

So if you are going to do a full-blown enterprise SEO audit, don’t feel like you have to tackle everything in one sitting. Spread it out over two months if needed (assuming the client’s expectations are aligned), and give each section the attention it deserves. After all, these audits will lay the foundation for everything that follows; it’s worth taking the time that’s needed to get them right.

Whether you’re flying solo or leading an in-house team, I hope that this framework will help you build an SEO strategy that’s not only data-driven but built to deliver real, measurable results!