Google was surely celebrating recently when Gartner reported that Android handsets outshipped Apple’s iPhone by close to a 2:1 margin. Given Apple’s head start in the market, it certainly is an impressive feat. But Google may regret the strategic choices that have led to this victory over Apple. To achieve the “win,” Google may have unwittingly created and trained a mercenary army of hardware manufacturers, willing to sell themselves to the highest bidder—whether that be Google, Baidu or Bing.

There is no doubt that Google understands the importance of the mobile web. A large part of Google’s future will rely on advertising revenue driven by mobile devices, which is likely a key reason why Google decided to go into competition with its one-time ally, Apple.

To be an effective competitor to iOS and the iPhone phenomenon, Google had to make some important choices around Android’s business model. Emulating aspects of Microsoft’s Windows strategy, Google chose to focus on providing its mobile operating system to as many hardware vendors as possible. But unlike Microsoft, Google makes money off advertising, not software. Google didn’t have to rely on Android directly generating revenue; they just needed it to drive search traffic.

So Google decided to give Android away to anyone who wanted it—and from this, the Open Handset Alliance was born. What had been traditionally the hardest part of making a phone—building a decent operating system—not only became easy, it became free. Google even went to the extent of open sourcing the entire effort. Take that, Apple. Unsurprisingly, the manufacturers tripped over themselves to sign up.

This began a very successful war against Google’s erstwhile partner, Apple. Google didn’t have to do any of the fighting—the Open Handset Alliance hardware manufacturers did it all for them. Without having to build a single phone (though Google did try, unsuccessfully), Android took volume leadership in the smartphone space. And Google gets to sit back and watch, hands clean, while its search traffic explodes.

But Google might soon find the many third parties it has relied on to battle Apple have instead become a much greater threat than Apple ever was.

The first signs of trouble brewing came out of China. Earlier this year, when Google looked like they were going to withdraw from China altogether, a number of Open Handset Alliance manufacturers realized they could be left selling smartphones in China without access to a number of key smartphone services that Google had traditionally supplied. So they started to look for replacements to Google’s services. The open-source nature of Android made that possible. More recently, Baidu, the internet search engine that has successfully challenged Google for ownership of the Chinese market, has taken an even bolder approach. It’s reportedly in negotiations with a number of smartphone manufacturers to remove all references to Google, and replace them with Baidu.

That was bad news. But what should really have Google concerned, however, is that there are instances of this fight being moved to domestic soil. Microsoft recently negotiated with Verizon that some of the Android phones that ship to Verizon customers will have Microsoft’s Bing, not Google, as the default search engine. And the manufacturers are getting in on the act too: Motorola recently released a new phone, the Citrus, based on Android, but shipping with Bing.

Yes, it’s Google’s operating system. In both these instances, it counts as a “win” in the handset volume war against Apple, Microsoft, Nokia and RIM. But Google will not make a cent on this handset, despite having enabled its creation with Android. All the search revenue will flow to Microsoft.

What’s the endgame here? Well, with both handset manufacturers and networks increasingly becoming commoditized, each are desperate to find new sources of revenue. Between them, the most valuable thing they have is control over what goes on the phone right before it reaches the customer: what apps, and what search. This is exactly what Google needs to control as the future shifts to the mobile web.

Google is losing this fight. It’s a poorly kept secret that Google now has to pay Apple — and pay Apple a lot — to keep Google as the default search engine on the iPhone. It won’t be long before Google’s “allies” in the Open Handset Alliance — the manufacturers making Android phones — realize that Google need them a lot more than they need Google, and auction off the default search services on the phones they ship. Google may have no choice but to buy their support, too. And it surely won’t come cheap.

The Android operating system is, as Google initially intended, untethered to any particular partner. This was a smart way of fighting the opening battles of the smartphone wars against Apple. Whether it proves to be a profitable way of conquering the mobile search business is an open question.

James Allworth is a Fellow at the Forum for Growth and Innovation at Harvard Business School.