What Might Go Wrong When Working With An Ecommerce SEO Agency

TL;DR:

SEO can transform your ecommerce business, but it’s not without risk. From unrealistic expectations to algorithm shifts and poor agency partnerships, a lot can go wrong. This blog post explores what to watch for and how to build a transparent, results-driven relationship with your SEO partner that fuels long-term growth.

Understanding the Volatile Nature of Ecommerce SEO

In my honest opinion, search engine optimization (SEO) is one of the most powerful growth levers for e-commerce brands, but it’s not necessarily a magic bullet by any means. With SEO, keyword rankings fluctuate, algorithms change all the time, and competition intensifies daily. What worked to rank brands six months ago, or even last month, may not work tomorrow.

Success in ecommerce SEO comes down to managing the things you can control, which include your strategy, the quality of your content (category/product pages and blog posts), site structure, and partnerships, while building resilience against the things you can’t control.

I wrote this post to help you explore what might go wrong when working with an ecommerce SEO agency, how to identify red flags before signing an agreement, and how to build a relationship that drives sustainable growth, not short-term vanity wins.

The Single Biggest Mistake Companies Make with SEO

I have been managing SEO clients, either directly or indirectly, for the better part of 16 years. Most businesses, ecommerce or not, fail because the agency they chose to do their SEO set really bad or unrealistic expectations. That will kill you… dead in the water.

And I won’t lie, I have been the guy who has set some of those poor expectations early in my career. Many agencies will tell you what you want to hear to close the deal, and that’s really bad business, and it NEVER ends well.

In my opinion, the single biggest mistake that ecommerce companies make with their SEO is treating it as a one-time project or quick fix… not a long-term business investment, which it 100% is.

This disconnect creates a slew of problems for brands:

  • Impatience for Results: They expect meaningful traffic growth in 30 days instead of 6-12 months.
  • Tracking Vanity Metrics: They celebrate keyword rankings instead of focusing on sales, conversions, and lifetime value.
  • Lack of Integration: They run SEO in a silo instead of tying it to paid search, CRO, and customer insights.

I’ve seen it so many times, when brands expect instant gratification, they pressure their agency into chasing short-term wins (like keyword stuffing or irrelevant backlinks) that hurt long-term performance. This only creates more problems, often times, including penalties that are hard to reverse. It’s no bueno.

The Reality of SEO Timelines: A Marathon, Not a Sprint

At the end of the day, you need to understand and accept that good, sustainable SEO takes time, especially for ecommerce websites. Think about it, you must get the search engines to your website and have them crawl and index you, you have to build topical authority through strong, helpful content, and build third-party validation and credibility through backlinking and citation building.

This takes a minute… results rarely appear overnight, unless you are a well-known, recognized, massive brand.

Here’s what a realistic timeline actually looks like:

  • First 3 Months: Technical cleanup, keyword mapping, and content planning.
  • 3 – 6 Months: Early signs of improvement… better indexing, rising impressions, and modest ranking gains.
  • 6 – 12 Months: Significant traction, improved conversions, and stronger visibility for priority categories.

It’s also important to understand that SEO success compounds over time, much like compounding interest. The brands that win are those that commit to consistent effort, data-driven iteration, and patience.

Now that expectations and timeline are out of the way, let’s talk about some of the external and internal risks that could cause things to go sideways on you in a hurry.

External Risks: Why You Can’t Control Everything in SEO

Even the best ecommerce SEO agency can’t control everything. There are always going to be uncontrollables. External factors, especially Google’s ever-changing algorithms, play a massive role in your organic performance, so it’s important to understand them.

Google Algorithm Updates

If you didn’t know, Google updates its search algorithms (how it decides who should rank for which search queries) thousands of times each year. Fortunately, the majority of these are minor, but some are massive and are capable of shifting entire industries overnight. I’ve seen this happen so many times.

Here are some examples of the big ones:

  • Panda (2011) targeted thin content and content farms, decimating low-quality sites.
  • Penguin (2012) punished manipulative link schemes.
  • Core Updates (2019–2025) have increasingly focused on E-E-A-T (Experience, Expertise, Authoritativeness, and Trustworthiness).

These updates typically hit without warning, and when they do, even well-optimized ecommerce sites can experience ranking drops. That doesn’t mean your agency failed; it means that Google changed the rules mid-game and now we have to change strategy.

When this happens, the best agencies focus on adaptation and recovery:

  • Monitoring algorithm chatter through Google Search Central, Reddit, and forums.
  • Conducting impact audits through web crawlers like Ahrefs and Screaming Frog.
  • Updating on-site content and link strategies.
  • Prioritizing quality signals and user experience over shortcuts.

Internal Risks: Pitfalls in Your Ecommerce SEO Strategy

While external factors create uncertainty, most SEO breakdowns come from internal missteps, either strategic, technical, or creative. Let’s dive into each.

Using ‘Black-Hat’ Tactics and Facing Penalties

In an effort to deliver fast results, some agencies still rely on black-hat SEO tactics such as:

  • Buying or exchanging spammy backlinks
  • Keyword stuffing product descriptions
  • Cloaking or hiding text
  • Auto-generating low-quality pages

These shortcuts might offer short-lived ranking boosts but often trigger manual penalties or algorithmic penalties. Recovering from them is painful, sometimes requiring a full domain cleanup or rebrand. Legitimately, I’ve had brands come to me for help, and the answer is… burn it down and start over.

Quality ecommerce SEO strategies take longer but build long lasting, compounding results. They focus on white-hat tactics: earning backlinks, improving UX, and optimizing content for users, not search engines.

Neglecting the Technical Foundation of Your Ecommerce Site

Did you know that your website structure and code can make or break your SEO efforts? Most brands we work with run on Shopify and for the most part, they are technically sound. However, there are lots of ecommerce websites that don’t, and even world-class content with the best SEO won’t rank if your site’s foundation is broken. It’s seriously sad.

Some of the most common technical SEO issues include the following:

For ecommerce sites with hundreds or thousands of SKUs, even small technical issues can multiply across pages, wasting crawl budget and diluting SEO performance.

A great agency prioritizes quarterly crawls and technical audits to catch and fix issues early. We use Ahrefs crawler and have those scheduled out for each of our clients. When issues arise, we prioritize based on estimated impact and knock them out.

Focusing on Content Quantity Over Quality

This is a huge one, publishing more content instead of better content. It’s becoming an even bigger problem as of late since it’s so easy to “write” blog content using AI engines like ChatGPT (please don’t do this).

Many agencies churn out endless blog posts or thin category page descriptions just to “feed the algorithm”. But in ecommerce, quality content = content that is actually helpful and useful to the end user/reader.

Great ecommerce SEO content does the following:

  • Answers real customer questions (“which pendant lights look best over a large island”).
  • Helps shoppers compare brands and make confident purchase decisions.
  • Helps shoppers compare products and make confident purchase decisions.
  • Uses storytelling and visuals to elevate product pages.
  • Demonstrates authority through data, testimonials, or expert commentary.

Thin, repetitive, or AI-generated content does the exact opposite: it confuses search engines, bores customers, and erodes trust. You can clearly see why that’s a problem, right?

Google’s Helpful Content System and AI Overviews prioritize authenticity and expertise. Your content should reflect genuine brand knowledge and customer insight, which you can gather from customer research.

Choosing the Wrong SEO Agency: A Partnership Problem

In all of the years I’ve done this, I can confidently say that the very best SEO isn’t just a service that’s delivered by an agency, it’s a strong partnership between the agency and the client. The wrong agency relationship can tank your ROI faster than any algorithm update.

Red Flags: Unrealistic Guarantees and Lack of Transparency

If an agency promises “#1 rankings in 30 days” run away as fast as you possibly can.

No one controls Google. No one has a strategic partnership with Google. No one has an SEO contact at Google. These are all lies. Instead, the best agencies focus on measurable, business-aligned metrics impressions, organic sessions, and revenue generated.

Warning signs to look for:

  • Cookie-cutter campaigns without ecommerce specialization.
  • No clear reporting or visibility into deliverables.
  • Overemphasis on vanity KPIs.
  • Unwillingness to explain strategy or decisions.

A trustworthy agency prioritizes education and transparency, explaining not just WHAT they’re doing but WHY they are doing it. They tie SEO work directly to outcomes like improved category performance, reduced ad dependency, or higher customer lifetime value.

Misaligned Goals and Poor Communication

SEO works best when the client and agency are in sync. Misalignment happens when:

  • The brand expects traffic growth while the agency focuses on technical fixes.
  • The agency lacks access to product, inventory, or promotion data.
  • There’s no shared understanding of success metrics.

Regular check-ins, shared dashboards, and open Slack or ClickUp communication prevent this breakdown.

The best results happen when both sides collaborate, sharing insights from paid media and customer feedback to inform SEO decisions. Remember: SEO doesn’t live in isolation; it amplifies your broader marketing ecosystem.

Navigating the Bumps: A Proactive Approach to Ecommerce SEO

Please remember that SEO will never be a straight line… rankings fluctuate, competitors pivot, and algorithms evolve. But with the right agency and mindset, you can turn those bumps into momentum.

Here’s how:

  • Choose transparency over guarantees: Look for agencies that teach you what they’re doing and why.
  • Set realistic expectations: Commit to a 12-month horizon, not a 12-day miracle.
  • Integrate SEO with your broader marketing strategy: Paid, organic, and CRO work best together.
  • Prioritize long-term equity: Quality content and clean site architecture outperform quick hacks every time.
  • Stay informed: Follow Google’s official updates and keep your agency accountable for proactive adjustments.

The right ecommerce SEO partner will help you weather updates, outlast competitors, and build a brand that grows sustainably through organic search, no matter what changes tomorrow. The brands that win will be those that value transparency, patience, and alignment between marketing and customer intent.

If you would like a free SEO audit and roadmap, please reach out to us today.

Frequently Asked Questions

What is the main mistake companies make with SEO?

Treating SEO as a short-term project rather than a long-term investment. This leads to impatience, poor strategy, and reliance on risky tactics that harm sustainable growth.

How long does ecommerce SEO take to show results?

Most brands start seeing measurable traction between 6-12 months, depending on competition, site authority, and how well the strategy is executed.

Can Google algorithm updates ruin SEO progress?

They can temporarily impact rankings, but a quality SEO agency adapts, audits changes, and updates strategy to recover performance over time.

How can I tell if my SEO agency is doing a good job?

Look for transparent reporting tied to revenue, organic traffic quality, and conversions, not just rankings. A good agency educates you, communicates clearly, and shows how SEO impacts your bottom line.

What’s the safest way to grow my ecommerce site with SEO?

Stick with white-hat practices: create helpful content, earn links naturally, improve site speed, and focus on user experience. Avoid shortcuts that could trigger penalties.

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