You started an LLC, someone told you to get QuickBooks, and now you are paying a monthly fee for a program with a hundred features you will never touch, plus another charge just to file your contractors’ 1099s. For a solo or very small LLC, that is a lot of cost and complexity for what is really a simple job: track your income and expenses, and record what you paid contractors so you can file 1099s at tax time.
Plenty of accounting tools do that job for less money and far less fuss, and several handle 1099 tracking without a bookkeeper. Here are five QuickBooks Online alternatives worth considering for a new LLC, and how to actually handle the 1099 side.
The short version
For a new, small LLC, QuickBooks Online is often overkill and its 1099 e-filing is an extra cost. Wave is the standout free option for a solo LLC, Xero is a full accounting tool that scales cleanly, Zoho Books is affordable and feature-rich with a free tier for low revenue, and FreshBooks is the simplest if invoicing is your main need. If you would rather not do the books at all, a managed service like Bench hands the whole thing to a human. Whichever you pick, the 1099 essentials are the same: collect a W-9 from each contractor before paying, track what you pay each one, and e-file 1099-NEC for anyone you paid 600 dollars or more, by the deadline.
Table of Contents
1. Wave
Wave is the best starting point for a solo LLC on a budget, because its core accounting and invoicing are free. You can track income and expenses, send invoices, and categorize contractor payments so you know who you paid and how much heading into tax season. Some extras, like payroll or 1099 filing, are paid, but for a one-person business that just needs clean books and a record of contractor payments, free is hard to argue with. It is the natural first stop before you pay for anything heavier.
2. Xero
Xero is a full double-entry accounting platform that many find cleaner and more approachable than QuickBooks, and it scales well if your LLC grows. It handles expenses, bank reconciliation, and reporting, and lets you track payments to contractors so you can pull the numbers you need for 1099s. It is a paid subscription, but competitively priced against QuickBooks, and its interface is friendlier for someone doing their own books. For an LLC that wants real accounting power without the QuickBooks feel, Xero is a strong pick.
3. Zoho Books
Zoho Books is the value choice: affordable, genuinely full-featured, and part of the broader Zoho suite if you use its other tools. It even offers a free tier for businesses under a certain revenue, which suits a brand-new LLC, and it tracks vendors and contractor payments cleanly for 1099 purposes. It does more than the simplest tools while costing less than QuickBooks. For a cost-conscious owner who still wants proper accounting features and room to grow, Zoho Books punches well above its price.
4. FreshBooks
FreshBooks is built around invoicing and simplicity, which makes it a comfortable fit for freelancers and service-based LLCs whose main need is billing clients and tracking expenses. It is easy to learn, tracks what you spend including payments to contractors, and stays out of your way. It is less of a heavy accounting engine than Xero or QuickBooks, which is the point. If your books are simple and your priority is getting paid and keeping tidy records without a learning curve, FreshBooks is the easy option.
5. Bench
If the honest answer is that you do not want to do the books at all, Bench takes a different approach: it is a managed bookkeeping service where real people handle your accounting for you. That is not “without a bookkeeper,” but it is worth knowing as the alternative for an owner who would rather hand off the whole task than learn software. It costs more than doing it yourself in an app, and less than a traditional accountant on retainer. For someone whose time is better spent on the business than on categorizing transactions, paying to make bookkeeping someone else’s job is a legitimate choice.
How to actually handle 1099s without a bookkeeper
The software is only half of it; the 1099 process is a few simple habits. First, before you pay any contractor, collect a completed W-9 from them, which gives you their taxpayer information and confirms whether they need a 1099. Track what you pay each contractor through the year in whichever tool you chose, so the totals are ready at tax time. Then, for any contractor you paid 600 dollars or more for services, e-file a 1099-NEC by the deadline, either through your accounting software if it offers it or through a dedicated 1099 e-filing service. The official rules and forms live at IRS.gov. None of this requires a bookkeeper, just doing it in order and not leaving the W-9 collection until January. For a related back-office pitfall worth avoiding, see our guide on how invoice spreadsheets cause duplicate charges.
This article is general information, not tax, accounting, or legal advice. Filing thresholds, forms, and deadlines change and your situation may differ, so confirm current requirements at IRS.gov and consult a CPA or tax professional about your LLC’s specific obligations.
Frequently asked questions
Do I need QuickBooks for a new LLC?
No. QuickBooks Online is powerful but often more than a new, small LLC needs, and its 1099 filing is a paid add-on. Simpler, cheaper tools like Wave, Xero, Zoho Books, or FreshBooks cover the core job of tracking income, expenses, and contractor payments for most solo and small LLCs.
What is the best free QuickBooks alternative for an LLC?
Wave is the standout free option, offering core accounting and invoicing at no cost, which suits a solo LLC well. Zoho Books also has a free tier for businesses under a certain revenue. Both let you track contractor payments, though some extras like payroll or 1099 e-filing may cost extra.
How do I track 1099 contractors without a bookkeeper?
Collect a W-9 from each contractor before paying them, record what you pay each one throughout the year in your accounting tool, and e-file a 1099-NEC for anyone you paid 600 dollars or more by the deadline. Doing it in that order, and not leaving W-9s until tax time, keeps it manageable yourself.
When do I have to file a 1099-NEC?
Generally when you have paid a contractor 600 dollars or more for services during the year, with the form due by the filing deadline in late January. Rules and thresholds can change, so confirm the current requirements at IRS.gov and check with a tax professional about your specific situation.
Can accounting software e-file 1099s for me?
Some can, often as a paid feature, and others let you export the totals to file elsewhere. If your chosen tool does not e-file 1099s, a dedicated 1099 e-filing service can do it from your tracked contractor payments. Check whether the feature is included or an add-on when you pick your software.
The bottom line
A new LLC rarely needs everything QuickBooks Online offers, and it certainly does not need to pay extra just to file a few 1099s. Wave is the free starting point, Xero and Zoho Books give you real accounting for less, FreshBooks keeps invoicing simple, and Bench hands it all to a human if you prefer. Whatever you choose, collect W-9s up front, track contractor payments, and e-file 1099-NEC on time. For more on running the money side of a small business, browse The Other Stream’s Business section.
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