FreshBooks: Best alternative for invoicing and ecommerce software.Xero: Best overall QuickBooks alternative for small business accounting software.Whether you’ve become frustrated with your current QuickBooks subscription or you’re looking for accounting software for your new business, there are plenty of software for you to consider, including some free QuickBooks alternatives. The best QuickBooks alternative has all the necessary bookkeeping features small businesses need but is often easier to use and comes at a lower cost.