FORTUNE — It has not been a terrific year for eBay (EBAY), but more of a middling one. After years of restructuring the company and retooling its offerings, the e-commerce company seems to be hitting something of a soft patch that, while far from derailing its comeback, is taking a good amount of the wind out of it.

eBay’s stock is up 2% so far in 2013. Not bad in itself but lagging the Nasdaq’s 30% gain in the same period. eBay rival Amazon (AMZN) is also up 30%, while other big-name tech companies have rallied even higher: Google (GOOG) up 40%, Yahoo (YHOO) up 72%, and Facebook up 103%.

What’s holding eBay back relative to its large-cap peers in the consumer web industry? Part of it is that the company outperformed those same peers in 2011, when it gained 68% as CEO John Donahoe’s multi-year turnaround effort began to bear fruit and when eBay was one of the earliest tech companies to show it could make money on the mobile web.

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As a result, eBay is much less the auction-oriented site that was an online consumer fad a decade ago and is now a much more staid but larger company building an e-commerce and payments platform supporting legions of small retailers as well as a growing number of large ones like Home Depot (HD) and Macy’s (M).

eBay’s revenue grew 27% in 2011 and 21% last year (to $14.1 billion), but Wall Street analysts expect that growth to slow some this year, to about 14%. That has put the stock’s rally on pause as investors wait to see whether the turnaround can yield stronger growth in coming years.

When eBay reported its third-quarter earnings last week, investors were a little spooked by some comments by Donahoe and CFO Bob Swan. “The U.S. e-commerce softened considerably, and we have a cautious outlook for the holiday season,” Swan said, explaining the company’s guidance for 80 cents a share in fourth-quarter earnings, which was below Wall Street’s consensus figure of 83 cents a share.

In the conference call to discuss earnings, Swan elaborated:

“The thing that’s caused us the most angst is what we believe is a dramatically decelerating U.S. e-commerce growth rate from the second quarter of 15.5% to 16% for comScore to the third quarter of closer to 13% … We haven’t really seen any more positive signs in October than what we experienced through the latter part of the third quarter in the U.S.”

Such comments set eBay’s stock sinking until Donahoe, who himself referenced “a fairly lackluster macro environment” in the earnings call, said the next day that those comments were intended to be conservative and not as negative as they came across. ““I don’t think we are seeing anything different than others are seeing; we just report first,” Donahoe said in an interview with AllThingsD.

That’s not encouraging news for the fourth quarter — by far the busiest for nearly all online retailers — but it doesn’t mean eBay’s turnaround is in trouble. There are, however, other concerning signs — especially in mobile commerce, a key area of the company’s growth. While eBay acquired 36% of its new customers last quarter through mobile devices, they spent less because they are younger and with less disposable income or because they are living in emerging economies.

A bigger and more immediate concern in the rising competition in e-commerce: eBay and Amazon have long been rivals, but as their business models expand, they are beginning to encroach on each other’s traditional turfs. This month, Amazon launched “Login and Pay,” which lets Amazon’s 215 million active customers use Amazon’s technology to pay for purchases on other sites. Amazon earlier unveiled Checkout by Amazon for physical retail stores. Both of these new services will compete directly with eBay’s areas of growth.

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PayPal has faced down competitors like Google Wallet before and maintained its edge. Building an online payments product is such a long and complex process that first-mover advantage is substantial. Nor is eBay taking Amazon’s moves sitting down. Its PayPal subsidiary announced this month a service offering free two-day shipping (just like Amazon Prime) for purchases made on retail sites such as Levi’s, Kenneth Cole, and Sports Authority.

Even as eBay battles it out with Amazon, it’s facing competition from a new wave of retailers like Groupon Goods (GRPN), Etsy, Fab, Zulily, and many others. It may also face a formidable competitor in Alibaba if the Chinese e-commerce giant’s planned IPO in U.S. markets presages a move into global commerce. And PayPal faces upstarts like Square, which this month announced a service letting anyone with a debit card send cash by email.

eBay recently responded to rising competition in online payments by paying $800 million for Braintree, an online payments processing company popular with mobile developers and growing startups like Airbnb and Uber. Donahoe has said the acquisition will strengthen PayPal’s global presence in mobile commerce. And Monday, eBay bought London-based Shutl to help it offer same-day deliveries in as many as 25 cities by the end of next year.

Such moves are likely to keep eBay growing in a competitive market. More worrisome is that competition is intensifying in e-commerce just as economic uncertainty is slowing the pace of e-commerce growth. Even if it continues to make shrewd moves, eBay investors may find the turnaround it took years to put into place may not be producing the rich crop of fruits they once anticipated.