If you’ve been waiting to ditch your desktop accounting software for a Web-based application, Microsoft may have given you a good reason to do it sooner rather than later.

The software giant disclosed last week that after November 16 it will stop selling its Microsoft Office Accountant software line, including both desktop and online versions – thus ending its long battle to compete effectively with Intuit’s QuickBooks programs.

For soon-to-be-former Office Accountant users, or anyone who’s in the market for a new way to send invoices, track expenses and create profit and loss reports, a Web-based app may be the way to go.

The past few years has seen an influx of Web-based accounting and bookkeeping apps from established players -including Intuit, which sells a Web-based version of QuickBooks called Quickbooks Online. They’ve been joined by online-only start ups such as Clarity Accounting, Less Accounting and Numia.biz, and open source or shareware programs such as GnuCash and LedgerSMB.

On the plus side, Web-based programs live “in the cloud,” meaning program and data files live on a server connected to the Internet and can be accessed through a browser from a PC or smartphone anywhere there’s an Internet connection. Most are subscription-based, with users paying either a flat annual fee or monthly subscription.

Some desktop software fans remain unswayed by the online innovation. Kathleen Schneibel, a Minneapolis CPA who providing accounting services for small businesses, says she’s not comfortable putting that much of her clients’ financial information on someone else’s servers. Schneibel, who worked as a company controller before hanging out a shingle three years ago, says if someone wants 24/7 access to financial records, why not just keep the program on a laptop? “And if you’re paying someone  each month you’ll end up paying way more than if you just bought it yourself,” she says.

But Jeff Nicol, a contract chief privacy officer in Hood River, Oregon, affirmed his belief that Web-based is the way to go after using both types of programs over the past year. Nicol has used QuickBooks Online for his own business, Privacy Ready LLC, for some years. He likes the convenience of being able to share information with his accountant without needing to burn the files onto a CD. “It makes it really easy to interface with her when it’s tax time,” Nicol says. What’s more, upgrades happen without him having to do anything, and he doesn’t have to worry about backing up his computer to protect data from being lost. “You just turn it on and it’s there,” he says.

Then Nicol took over as secretary and treasurer of a Hood River-based non-profit business group, the Columbia River Gorge Technology Alliance, and assumed the responsibility for their financial records, which had been created on QuickBooks’ desktop version. That meant Nicol had to buy the software, install it on his computer, import and set up the files.

For general peace of mind, he subscribed to an online back-up service to run regular saves on the data. “It’s definitely more work for me,” he says. Sharing information is harder too, since he has to email it to fellow board members rather than letting them to look at it online. Says Nicol: “If I were on vacation or got hit by a truck, I’d be a bottleneck, not because I want to be, but by the nature of having the software sitting on my machine.”

Meanwhile, if you’re currently a Microsoft Accountant customers, a FAQ posted on the Microsoft website suggests that free Excel templates packaged with Microsoft Office are “a better option” for small businesses. Microsoft will stop supporting add-on services for the program from eBay and Equifax on Dec. 15, but will continue offering users phone help for five years, though exactly how long depends on what version of the software they use and how long ago they bought it. Anyone who bought the program within in the past 30 days can get a refund.