Running an e-commerce store comes with many unique challenges, from behind-the-scenes logistics issues, dealing with customers to acquiring traffic profitably.
And finding a reliable ecommerce SEO agency who can drive real revenue growth adds to those challenges.
P.S if you are new to SEO, consider reading our guide on What is SEO? before reading this guide.
Unique challenges of Ecommerce SEO
If we consider just one slice of acquiring traffic – organic traffic, that also for ecommerce stores offers a unique challenge in that ecommerce stores are generally large, complex and constantly changing.
It’s easy to get buried in the SEO tasks that need to be done and lose focus on what’s important and what will ultimately move the needle.
In this guide we’ll talk about:
- What some of those unique ecommerce SEO challenges are
- How your platform (CMS) choice can help or hinder
- How to choose a partner to work with on your SEO ecommerce journey
- What the expected outcome of investing in SEO might be
What are examples of specific ecommerce SEO challenges?
A generalist SEO approach doesn’t work well when it comes to ecommerce, whereas an experienced ecommerce SEO agency will know exactly what to prioritise, and what will move the needle.
For example we commonly see these specific ecommerce SEO related issues, that a general approach wouldn’t account for:
- Complicated keyword cannibalisation issues that consistently need to be addressed
- Product removal and how to deal with valuable product URLs
- Adequate keyword targeting of category pages
- Search intent opportunities being missed due to poor keyword research
- Off the shelf CMS issues that hold back progress
These are the types of ecommerce specific issues we see and fix day in day out at my ecommerce SEO specific agency – Searchant.
Unless you are working with an ecommerce SEO specialist, these types of issues generally go unnoticed and unresolved, ultimately limiting the growth of a store.
Fundamentals of Ecommerce SEO
Creating an ecommerce store that looks beautiful is less of a challenge than it used to be; themes that look great can be tweaked to give a great looking store that also has great user experience.
But while stores can easily look great, they can often have underlying technical SEO issues, and having a store that looks great is just the beginning and a point in which many novice ecommerce store owners get stuck.
Acquiring traffic profitability is where the real work starts.
Typically even newer store owners understand they need SEO but have very little idea where to start with it, often doing SEO themselves to begin with and having limited success or very slow progress.
Or paying someone to do SEO for them that actually turns out to be helping, or even causing more harm than good.
For new stores there is also a unique challenge that SEO isn’t always the best channel to get your store off the ground with, generally speaking getting ads profitable to begin with, to prove market fit, then using that profit to invest properly into SEO is the best route into having a successful SEO campaign.
If SEO is the first channel and HAS to be successful then it’s common store owners give up on it too early, as results for new stores can take multiple years depending on the difficulty of the niche.
So before we talk about where to start with SEO, let’s go back a step..
How to think about your ecommerce platform
The platform or CMS you choose can make or break your ecommerce success.
Most stores start out with an off the shelf solution for their CMS, such as Shopify or WooCommerce, each of those platforms comes with their own set of benefits & challenges.
You may even decide to go the custom cart route and create their store from scratch or from another existing framework.
There is no right or wrong CMS/framework to use, but here are some considerations and specific issues with some of those choices that might not be immediately apparent when making those decisions:
What innate SEO limitations or restrictions do those platforms have?
For example, Shopify out of the box has various settings that limit SEO performance, if store owners aren’t aware of those issues, performance is limited.
How quickly can you make changes on those platforms
If your store requires a developer to make simple changes, then over time compared to competitors who are on a more agile platform you will lose out, those delays may not seem major but compound those delays over a number of years, and you get left behind while others stores can implement and capatalize on opportunities significantly more quickly.
How do Search Engines and AI treat your platform?
This is a bit of a hidden factor, but we see clearly in our data that some platforms are just preferred over others, this is likely due to the underlying architecture of the platforms, the overall sentiment that search engines have towards platforms (think of it a bit like email reputation).
How quickly does your platform adapt to changes in the marketing landscape?
This is a bigger one that you might imagine, some of the big ecommerce CMS platforms are constantly building partnerships with other platforms to make your store better, more visible, or more connected, without having to implement custom solutions on your own. Standing on the shoulder of giants is an easy way
These questions and many more like them, typically only occur to ecommerce brands once they are already into a platforms and they are starting to learn about the restrictions and limitations, so hopefully these questions provide a bit of a guide to help you consider how your platform choice may impact the long term success of your store, and also avoid a few headaches along the way.
Here’s an example comparison of just those 3 options we discussed here, this is a simplification, there are many more factors and many more platforms to actually consider:

Choosing an SEO Ecommerce Partner
E-commerce SEO differs significantly from other forms of SEO, such as local SEO or lead generation SEO, and presents its own set of challenges, including how Google treats websites and how human behavior affects conversion rates.
Anyone can claim they know what they are doing, but can they actually show you?
SEO Agencies that know what they are doing will be able to back any bold claims or theories they have with data, such as case studies, a portfolio of clients, and even research.
Before you hire any SEO agency, you should ask them if they have:
- Case studies from previous clients showing how they helped them
- Any research where they have completed in-depth reports on ideas or industry changes
- Portfolio of clients in the e-commerce niche
Combining this information will give you a solid foundation before hiring them, ensuring they can back their talk with action. It also provides insight into whether they are a good fit for your online e-commerce store.
E-commerce SEO is about more than rankings; it comes down to one thing: revenue. After all clicks are good, but if the revenue is not flowing, then the business does not make any money.

Countless e-commerce brands get stuck focusing on driving organic traffic, most of which is vanity clicks. While clicks to blogs and informational pages are beneficial and look good on a graph, if they are not ultimately driving revenue, the SEO strategy is doomed from the start.
This is why a solid SEO strategy should always begin with examining keywords, more importantly, “money keywords” – the keywords that will not only drive traffic but ultimately drive revenue.
For example, a blog about the top 10 running shoes might attract 1000 clicks a month, but how likely is that blog to convert?

Whereas a solid collection page aimed at men’s running shoes might only drive 250 clicks a month, it could lead to a much higher conversion rate, as it is a very targeted, intent-based keyword.
You can even go much deeper on this and aim for even longer tail keywords, such as “Green Men’s Running Shoes,” which might receive fewer than 50 clicks a month, but as it is a very detailed search, it has a much higher chance of leading to a sale.
Knowing which keywords to target from day one for each page, collection, and product is crucial for any e-commerce store owner, as well as understanding the challenges each page faces, including technical SEO and UX issues, and how to address these issues to drive more sales.
What might the ROI be like when focusing on ecommerce SEO?
The million dollar question(s) when considering to start an SEO effort is, what will the ROI be, and when will it come.
It’s an obvious, and good question to ask, but is not an easy one to answer.
Before even starting to ballpark and answer to that question, we must understand:
- What is the current situation (how established is the store SEO wise)
- How quickly can the stores team address any technical issues that are brought up
- How competitive is the landscape currently
- How quickly are competitors moving
By starting to answer some of those questions, it’s possible to put forward an approximation or projection of where we can be, by when, but it is important to highlight, it’s will only ever be a projection, there are simply too many moving parts to give an accurate, precise prediction of where the store could get to.
Ultimately a better question to ask is – what is the overall potential for SEO as a channel for your store, and what will it take to get there.
For example if we can see a competitor is doing x10 the amount of targeted organic traffic, then what are the gaps we need to close, what are the technical, content and link gaps.
Once you have an understanding of that you can start to reverse engineer, but you will always be going after a moving target, and you don’t know for sure how fast that moving target is going.
Longterm, SEO (and it’s future incarnations including AI search) should typically be the biggest and best channel for ecommerce stores, if it is investing in correctly, and it will typically give the best long term ROI of any channel.
It may take 3 years of serious investment to get it where it needs to be, then that investment could be eased off and that may be the period of time when the ROI really kicks in.

And that is one of the main reasons why SEO isn’t always the best first channel to get to profitability and also why a lot of brands give on SEO and write it off, because they simply don’t invest in it for long enough to be competitive. E-commerce SEO Frequently Asked Questions
E-commerce SEO Frequently Asked Questions
Getting Started
Should I start with SEO or paid ads for my new e-commerce store?
For new stores, it’s generally recommended to start with paid advertising to prove market fit and generate initial revenue. Once you have profitable ads running, you can reinvest those profits into a proper SEO campaign. SEO results for new stores can take multiple years, especially in competitive niches, so having another revenue stream helps sustain the business while SEO builds momentum.
How is e-commerce SEO different from regular SEO?
E-commerce SEO faces unique challenges including complex keyword cannibalization issues, managing product URL changes when items are discontinued, optimizing large and constantly changing catalogs, and dealing with platform-specific technical limitations. It also focuses heavily on “money keywords” that drive revenue rather than just traffic.
How long does it take to see results from e-commerce SEO?
Results vary significantly based on your store’s current state, competition level, and niche difficulty. New stores should expect to invest seriously for 2-3 years before seeing substantial results. However, some improvements can be seen earlier – it’s just that meaningful, competitive rankings typically require sustained long-term investment.
Strategy and Keywords
What are “money keywords” and why are they important?
Money keywords are search terms that directly drive revenue, not just traffic. For example, “men’s running shoes” (a collection page) might get fewer clicks than “top 10 running shoes” (a blog post), but the collection page is more likely to convert because it targets users with purchase intent. Focusing on these revenue-driving keywords is crucial for ROI.
How do I avoid keyword cannibalization in my e-commerce store?
Keyword cannibalization is common in e-commerce due to similar products and categories. Work with an e-commerce SEO specialist to conduct proper keyword mapping, ensure each page targets unique primary keywords, and regularly audit your site for pages competing against each other for the same terms.
Should I focus on broad keywords or long-tail keywords?
Both are important, but long-tail keywords often provide better ROI for e-commerce. “Green men’s running shoes” might only get 50 clicks monthly but has higher conversion potential than broader terms. Start with longer-tail, more specific keywords that match exact purchase intent, then gradually work toward broader terms as your authority grows.
Technical and Platform Considerations
Does my e-commerce platform choice affect SEO performance?
Absolutely. Each platform has different SEO capabilities and limitations. Shopify, for example, has certain out-of-the-box settings that can limit SEO performance if not properly configured. Some platforms are preferred by search engines due to their architecture and overall reputation. Consider factors like ease of making changes, innate SEO limitations, and how quickly the platform adapts to marketing changes.
What technical SEO issues are common in e-commerce stores?
Common issues include inadequate keyword targeting on category pages, problems with discontinued product URLs, off-the-shelf CMS limitations, poor site architecture for large catalogs, and missing search intent opportunities due to inadequate keyword research. Many of these require e-commerce SEO specialists to identify and resolve.
How important is it to be able to make quick changes to my store?
Very important. If your platform requires a developer for simple changes, you’ll fall behind competitors who can implement opportunities quickly. These delays compound over time, potentially costing significant market share and revenue.
ROI and Investment
What kind of ROI can I expect from e-commerce SEO?
ROI varies widely based on current store status, competition, and investment level. Rather than focusing on precise predictions (which are impossible due to many variables), ask: “What’s the potential, and what will it take to get there?” Look at successful competitors to understand the opportunity size, then reverse-engineer the gaps you need to close.
How much should I invest in e-commerce SEO?
SEO typically requires serious investment for 2-3 years to become truly competitive. After this period, investment can often be reduced while ROI increases significantly. Long-term, SEO should become your biggest and best channel if invested in correctly, providing the best long-term ROI of any marketing channel.
When should I expect to break even on my SEO investment?
Most e-commerce stores need to think of SEO as a long-term investment. The heavy investment period is typically the first 2-3 years, after which the ROI really kicks in as you can reduce investment while maintaining and growing results. This is why many brands give up too early – they don’t invest long enough to become competitive.
Choosing an SEO Agency
How do I know if an SEO agency understands e-commerce?
Ask for specific e-commerce case studies, a portfolio of e-commerce clients, and original research they’ve conducted in the e-commerce space. They should be able to back any claims with data and demonstrate understanding of e-commerce-specific challenges like product management, category optimization, and revenue-focused keyword strategies.
What should I look for in an e-commerce SEO specialist?
Look for agencies that can show concrete results with data, have specific e-commerce experience, understand the unique challenges of your platform, and focus on revenue generation rather than just traffic. They should understand technical e-commerce SEO issues and have a track record of solving complex problems like keyword cannibalization and large-scale site optimization.
What questions should I ask potential SEO agencies?
Key questions include: Do you have case studies from e-commerce clients? Can you show research you’ve conducted on e-commerce SEO? What’s your experience with my specific platform? How do you handle common e-commerce SEO challenges like keyword cannibalization and product URL management? How do you measure and report on revenue impact, not just traffic?
Common Mistakes
Why do many e-commerce stores fail at SEO?
Common reasons include focusing on vanity metrics (traffic) instead of revenue, giving up too early before seeing results, not investing enough initially, working with generalist SEO agencies who don’t understand e-commerce challenges, and not addressing platform-specific technical issues that limit performance.
Should I try to do e-commerce SEO myself?
While basic SEO can be learned, e-commerce SEO involves complex technical challenges, large-scale optimization, and platform-specific issues that typically require specialist knowledge. Many store owners try DIY SEO with limited success, or accidentally hire agencies that cause more harm than good. Consider your learning curve, time investment, and opportunity cost versus working with specialists.
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