Unfortunately, yes it can. Let me explain.
Suppose your website is relatively new, and you currently only rank for a few terms, namely your brand name. After a year or so of optimizing your site for search engines, you notice that despite a huge increase in search traffic, your conversion rate is significantly lower than it used to be. What happened?
Unfortunately, the SE’s are not as smart as we think they are. Occasionally, they will rank your website for keywords that are completely irrelevant or too broad for your business. For example, I have a client who retails a highly niche clothing type. After about 2 years of SEO, they currently rank first page on Google for the broad search term “clothing stores”. However, looking at the web analytics, I found that not a single visitor from this keyword has converted to a sale.
I would venture to guess that most sites rank for several major keywords and many long tail keywords that are either too broad or have nothing to do with their website. So what’s the big deal? Nothing really, express your conversion rate will suffer.
From a birds eye view, it would be very disconcerting for an executive to see the conversion rate fall after beginning an SEO campaign. However, this is completely normal. It’s important to delve deeper into the analytics and monitor not just the overall conversion rate, but the individual conversion rates from SE’s, direct traffic, and referring sites.
It’s important not to obsess too much over conversion rates. If overall conversions (sales) are up, yet the conversion rate is down due to some external factor, there is absolutely no cause for alarm.