It started innocently enough with a March 22 announcement from Mailchimp announcing that it had asked Shopify (NYSE:SHOP) to remove the Mailchimp for Shopify app from the Shopify App Store. Both parties argued their cases in the court of public appeal. Regardless of who’s right in this little skirmish, the bigger implications for Shopify stock could be significant.

Here’s why.

On the surface, Shopify customers are merely losing one app out of countless others. May 12 was the last day of the company’s old Partner Program Agreement. Mailchimp was concerned about its email customers’ privacy under the new terms of the agreement, so it pulled its app from the Shopify App Store.

Shopify Stock and Mailchimp

“For months, we’ve been trying to work with Shopify on terms that would be fair and equitable for both of our businesses. Throughout these negotiations, we refused to agree to terms that jeopardize our users’ privacy and require us to hand over customer data acquired outside of Shopify,” Mailchimp said about its Shopify partnership .

For Shopify’s part, it hasn’t had a lot of good things to say about Mailchimp.

“It’s critical for our merchants to have accurate, complete insight into their businesses and customers, and this isn’t possible when Mailchimp locks in their data,” Shopify said. “Specifically, Mailchimp refuses to synchronize customer information captured on merchants’ online stores and email opt-out preferences. As a result, our merchants, other apps, and partner ecosystem can’t reliably serve their customers or comply with privacy legislation.”

It’s a classic “he said, she said” scenario.

Shopify users will still be able to use a third-party integration such as ShopSync or Zapier to sync data from Mailchimp although the reviews so far have been anything but positive. Shopify is pushing its users to other email marketing services that integrate with Shopify.

Meanwhile, small businesses that rely on out-of-the-box solutions for their integration are left scrambling to keep their businesses fully operational.

Square’s Threat to Shopify Stock

If this were just an issue of privacy, I’m sure Mailchimp and Shopify could figure out a way to meet both their users’ privacy concerns without blowing up the partnership.

However, this appears to be more about Shopify protecting its turf.

Mailchimp partnered with Square (NYSE:SQ) in November to offer ecommerce landing pages. Previously, Mailchimp provided landing pages that were used to collect email addresses or link to a company’s store. With the partnership with Square, its customers will be able to build pre-designed templates with ecommerce features including a shopping cart and built-in payment services.

Now, if Mailchimp were the only app that was seeking to leverage its existing services to provide a complete one-stop-shop e-commerce solution, I don’t think Shopify would protest nearly as much.

Clearly, CEO Tobi Lutke and the rest of the management team are concerned that Mailchimp could become a Trojan horse, causing other apps in the Shopify App Store to follow suit.

If enough businesses do this, putting Shopify users in a position of having to find new or band-aid solutions for their various services, Shopify’s position of strength could become its position of weakness.

I’m not saying that will happen, but it’s hard not to think Mailchimp’s become Shopify’s kryptonite.

The Bottom Line on Shopify Stock

InvestorPlace feature writer James Brumley recently had some very complimentary things to say about Shopify’s business model:

“The advent of a true, customer-centric and complete turn-key solution for aspiring entrepreneurs was inevitable. The industry had been getting closer to the right answer; Wix.com (NASDAQ:WIX) is a respectable rival Shopify should keep an eye on…There’s little doubt, though, that Shopify has finally found the precise pulse of what online entrepreneurs are truly looking for.”

Square is a more significant threat to Shopify than Wix because it’s already figured out how to help small- and medium-sized businesses in the brick-and-mortar world. Moving to help those customers capture more e-commerce business is a natural transition.

The Mailchimp skirmish with Shopify might turn out to be much ado about nothing.

However, it’s my experience that where there’s smoke, there’s fire. At 24 times sales, Shopify’s valuation assumes it’s full speed ahead. Be careful, or you just might get burned.   

At the time of this writing Will Ashworth did not hold a position in any of the aforementioned securities.