Looking for best accounting software for small business gets complicated when you're a startup, because most options were designed for established companies with predictable revenue and traditional banking. Your needs are different: you're tracking burn rate daily, connecting Stripe and corporate cards, managing both cash and accrual books for investors, and making decisions too fast to wait for monthly reports. The tools that work best for startups automate up to 98% of categorization, integrate natively with your fintech stack, and give you real-time metrics without requiring an accounting degree to interpret them.
TLDR:
Small business accounting software automates financial tracking, replacing manual spreadsheets with systems that handle transactions, reconciliation, and reporting. For startups, these tools provide real-time burn rate and runway visibility, connecting banks, payment processors like Stripe, and corporate cards. The best solutions automate up to 98% of categorization while maintaining accuracy through human oversight.
We ranked each tool on factors that matter for startups: AI automation that reduces manual categorization, integration quality with fintech tools like Stripe and Mercury, and startup-specific features including burn rate tracking and dual-basis accounting. Ease of use for non-accountants, real-time visibility, and transparent pricing also factored in. For accounting firms, we noted whether vendors compete through bookkeeping services. Assessments draw from vendor sites, user reviews, and public product information.
Puzzle is AI-native accounting software built for startups and the accounting firms that serve them. The system integrates natively with the fintech stack startups actually use, connecting to Stripe, Mercury, Ramp, Brex, and Gusto in minutes rather than requiring manual third-party configurations.
Bottom line: Puzzle delivers AI-native automation, real-time startup metrics, and native fintech integrations while partnering exclusively with accounting firms.
QuickBooks holds the largest market share but retrofits AI onto legacy architecture while competing with firms through QuickBooks Live.
QuickBooks offers invoicing, payroll, tax prep, reporting, and a third-party app ecosystem. Multiple pricing tiers range from Simple Start to Advanced, with strong brand recognition among accountants.
Good for established businesses with traditional banking and general accounting needs that don't require startup-specific metrics.
Limitations include direct competition with accounting firms via QuickBooks Live. Fintech integrations with Stripe, Mercury, and Ramp often need manual fixes. No native burn rate or runway tracking. Prices increased 64% to 83% over five years, with AI locked behind premium tiers.
Xero is cloud accounting software with a JAX AI assistant, built with stronger market presence in the UK, Australia, and New Zealand than in the United States. The platform offers bank reconciliation, invoicing, and many third-party app integrations.
Good for: International businesses needing multi-currency support and companies already embedded in Xero's global ecosystem.
Limitations: No native burn rate, runway, or ARR/MRR tracking. Stripe, Mercury, and other US fintech tools require third-party apps instead of native connections. JAX answers questions conversationally but doesn't drive deep automation for categorization or reconciliation. Xero sells directly to businesses instead of operating partner-only.
Bottom line: Strong international platform but missing US startup-specific metrics and native fintech integrations American companies need.
Zoho Books offers budget-friendly accounting for businesses in the Zoho ecosystem. It includes a free tier for companies under $50K revenue, plus invoicing, expense tracking, and bank reconciliation. The Zia AI assistant spans 55+ Zoho apps.
Good for: Businesses already using Zoho CRM or other Zoho products who need basic accounting.
Limitations: No burn rate, runway, or ARR/MRR tracking built in. Revenue recognition capabilities are limited. Templates aren't designed for SaaS companies or investor-ready financials that VCs expect.
Bottom line: Solid value for general businesses but missing the startup-specific metrics and automation tech companies need.
Digits offers autonomous accounting with AI agents that claim 97.8% accuracy across workflows. However, their full-service bookkeeping with in-house CPAs competes directly with accounting firms.
Self-serve starts at $100/month, full-service at $350+/month. Connects via Plaid with interactive reports and automated workflows.
Good for: General businesses across retail, healthcare, and consulting comfortable replacing their bookkeeper entirely.
Limitations: Competes with accounting firms for revenue. No native burn rate or runway tracking for startups.
Bottom line: Strong AI for general SMBs but wrong fit if you work with an accounting firm.
Rillet is an AI-native ERP for high-growth SaaS companies scaling toward IPO with complex multi-entity and revenue recognition needs. Features include multi-entity consolidation, ASC 606 revenue recognition, and partnerships with firms like Armanino.
Best for Series B+ companies with $50M+ ARR, multiple entities, and dedicated finance teams needing full ERP functionality.
Not right for pre-seed to Series A startups. Enterprise complexity and pricing exceed early-stage needs. Less focus on founder-first design and startup metrics like burn rate and runway.
Campfire targets mid-market tech companies outgrowing QuickBooks, serving as a NetSuite alternative with multi-entity consolidation and advanced revenue recognition. Built for 100+ employee companies with dedicated finance teams managing complex contracts and multi-currency operations.
Good for: Series A+ companies with 50 to 500+ employees, controllers and CFOs managing multiple legal entities with genuine ERP requirements.
Limitations: Implementation takes weeks instead of hours. Less focus on accounting firm partnerships. Missing founder-friendly dashboards and startup-specific metrics like burn rate and runway.
Bottom line: Full ERP for mid-market companies, not right-sized for earlier-stage startups.
Startups need accounting software built for their speed. Only 29% of small businesses close books in under a week, but founders make decisions daily.
Puzzle tracks burn rate, runway, and ARR/MRR automatically while categorizing transactions with up to 98% accuracy. Native Stripe, Mercury, and Ramp integrations work without manual workarounds. We partner exclusively with accounting firms and never compete for clients, giving you startup-specific metrics and real-time visibility when it matters most.
Your small business accounting software should work the way your startup does. Real-time dashboards and automated categorization mean you spend less time on bookkeeping and more time building your product. Software matters when it connects to your fintech stack without friction and gives you the metrics investors expect to see.
Puzzle works best for pre-seed to Series B startups needing burn rate, runway, and ARR/MRR tracking with native Stripe and Mercury integrations. QuickBooks fits established businesses with traditional banking, while Rillet and Campfire serve later-stage companies with multi-entity needs.
AI-native platforms like Puzzle and Digits automate categorization from the ground up, while QuickBooks and Xero retrofit AI onto older systems. Choose AI-native if you want up to 98% automated categorization and real-time dashboards; choose traditional if you need extensive third-party apps or already have complex QuickBooks workflows.
Startup-focused tools like Puzzle track burn rate, runway, and ARR/MRR natively with connections to Stripe, Mercury, and Ramp. General business software like Zoho Books and QuickBooks require third-party apps for fintech integrations and lack built-in startup metrics founders need for fundraising.
Puzzle operates partner-only and never offers bookkeeping services. QuickBooks competes directly through QuickBooks Live, and Digits offers full-service bookkeeping with in-house CPAs. Xero, Zoho Books, Rillet, and Campfire sell direct to businesses but don't provide competing services.
Move to an ERP like Rillet or Campfire when you hit Series B+, manage multiple legal entities, need complex revenue recognition across subsidiaries, or have 100+ employees with a dedicated finance team. Stay with accounting software like Puzzle or QuickBooks if you're pre-Series B with simpler needs.
