Best Accounting Software for Small Business 1. Intuit QuickBooks Online. 2. FreshBooks. 3. Wave. 4. Sage 50cloud. 5. Xero. 6. Zoho Books. 7. GoDaddy Bookkeeping. 8. Kashoo. 9. AccountEdge Pro. 10. OneUp. 11. Tipalti. 12. OnPay. 13. NetSuite ERP. 14. FreeAgent. 15. Accounting Seed. Top 9 Accounting Software Options for Small Businesses. Accounting Software. Best For. QuickBooks Online. (Best Overall) Most widely used small Which Accounting Software is Right for You? Which statement best describes you? What’s your budget for accounting software for your small business? Are Online Accounting Software for Small Businesses Running a business is not easy, especially when it comes to accounting. Mountains of Excel spreadsheets, shoeboxes full of receipts, different software for different tasks, frantic rushing during tax time; who wants this?