Top 6 Bookkeeping Software for Small Businesses in 2025

Starting a small business often means juggling receipts, invoices, and spreadsheets just to keep the numbers straight. At first, a simple sheet or notes app might do the job, but as things grow, it quickly becomes overwhelming, and mistakes start to creep in. 

That’s when the right bookkeeping software can make all the difference. 

Bookkeeping software won’t make you love accounting, but it can keep the chaos at a level where you can actually sleep at night without dreaming about your accountant giving you side looks. 

In this guide, we’ll walk through the Top 6 bookkeeping software for small businesses in 2025. You’ll see what each option offers, how much it costs, and the kind of business it fits best. By the end, you’ll know which bookkeeping software is right for you.

👉 Quick note: If you’d rather not deal with bookkeeping software at all, Haven has expert teams that handle your books, taxes, and more. That way, you can focus on running your business while we keep the numbers straight. Start with a quick strategy call here. 

Quick overview of the 5 best bookkeeping software for small businesses 

Before diving into each software in detail, see how they stack up side by side: 

1. Haven 

Haven is an all-in-one bookkeeping service for startups and growing businesses, paired with a modern dashboard we’ve built for our customers. 

When you work with Haven, you’re not left with spreadsheets or clunky reports. Instead, you see the numbers that matter most — profit & loss, cash flow, vendor spend, account balances, burn rate, and runway — in a clear, real-time view.

Haven Dashboard

What you get with Haven

• Monthly bookkeeping and reconciliations

• Categorization of business transactions

• Financial statements (P&L, balance sheet) prepared for you

• SaaS- and startup-specific accounting (like deferred revenue, accruals)

• Dedicated bookkeeper with CPA oversight

• Support that’s fast and built into Slack

Haven Dashboard showing expenses

Pricing

Plans start around $300/month for businesses spending $20K monthly, with pricing that scales based on revenue complexity (like crypto, inventory, or usage-based billing).

Haven pricing

Best For

Founders who want expert bookkeeping and tax support, along with a dashboard built for visibility and control. Haven is service-first, and the tool comes. Book a strategy call with Haven today and see how we can help. 

2. QuickBooks

QuickBooks is one of the most widely used bookkeeping and accounting tools. It’s popular with small and medium-sized businesses, freelancers, and solo business owners. It comes in both an online version (QuickBooks Online) and a desktop version. It helps handle day-to-day bookkeeping tasks, from tracking expenses to running reports.

G2 Rating: 4.0/5 (~3.5K reviews) 

QuickBooks dashboard

Key Features

• Automated bookkeeping: Syncs bank accounts and credit cards, sorts expenses, and reconciles accounts.

• Invoicing and payments: Create and send invoices, set up recurring bills, and accept online payments.

• Expense tracking: Track income, expenses, and mileage, with receipt scanning through the mobile app.

• Financial reporting: Run profit & loss, balance sheets, and cash flow reports.

• Inventory tools: Track stock levels and get alerts when items run low (in higher plans).

Pricing

QuickBooks Online starts at about $38/month for the basic plan and goes up to around $275/month for the Advanced plan with extra reporting and up to 25 users. Discounts are common. New users often get 50% off for the first 3 months or a 30-day free trial. Add-ons like payroll or live bookkeeping cost extra.

QuickBooks pricing plans

Who Should Use It

QuickBooks is a good fit for small to medium-sized businesses that want an all-in-one bookkeeping tool. It works well for people who want automation, easy reporting, and integrations with other apps.

3. Xero

Xero is a cloud-based accounting software built mainly for small and medium-sized businesses, sole traders, and freelancers. It focuses on being simple to use while offering powerful tools for bookkeeping, invoicing, and financial management. 

G2 rating: 4.3 out of 5 stars based on over 800 reviews

Xero dashboard

Key Features

• Bank connections: Syncs with 20,000+ banks for automatic transaction imports and reconciliation.

• Invoicing & payments: Send branded invoices, set reminders, and handle multi-currency payments with live exchange rates.

• Reporting: Profit & loss, balance sheet, and cash flow reports with customizable dashboards.

• Expenses: Upload receipts and manage reimbursements with Xero Expenses.

• Projects: Track jobs, quotes, time, and costs for accurate billing.

• Integrations: Connect with 1,000+ apps, including CRM and e-commerce platforms.

Pricing

Xero pricing plans cater to businesses at different growth stages, with unlimited users across all tiers, unlike QuickBooks’ user limits.

It has three main plans:

Xero pricing plans

All plans come with a 30-day free trial, and discounts may be offered from time to time.

Who Should Use Xero

Xero works well for business owners who want collaboration without limits. Since every plan includes unlimited users, it’s great if you have multiple team members or an outside accountant who needs access. It’s also a smart choice for companies working internationally, because of its strong multi-currency support.

4. Wave 

Wave is built with simplicity and affordability in mind, making it a favorite among freelancers and one-person businesses. Unlike most accounting platforms, Wave offers a free plan that covers unlimited invoicing, bookkeeping, and reporting, which is something rare in this space. The trade-off is that advanced features like payroll and discounted payment processing are only available in its Pro tier.

G2 Rating: 4.3/5 (306 reviews)

Wave dashboard

What You Get with Wave

• Connect bank accounts for automatic transaction imports and reconciliation.

• Create unlimited invoices and estimates with professional templates.

• Upload receipts via mobile and auto-categorize with OCR scanning.

• Generate profit & loss, balance sheets, and cash flow reports.

• Add payroll (from $20/month) and tax filing in select U.S. states.

• Work on the go with a mobile app for invoicing and expense tracking.

Pricing

Wave starts at $0 with the Starter plan, which includes most essentials. For more advanced features, the Pro plan runs $190/year (about $16/month), billed annually, and includes perks like auto-imported bank transactions and reduced payment processing fees.

Wave pricing plans

Who Should Use Wave

Wave is best for people who want to keep costs close to zero while still sending professional invoices and staying on top of expenses. If you’re a freelancer or just starting your business and want to know who owes you money and whether you’re profitable, Wave gives you exactly that. 

5. Sage 50

Sage 50 (formerly Sage 50cloud or Peachtree Accounting) is mainly a desktop-based accounting software, but it also has cloud features so you can back up data and access it remotely. It’s designed for small to medium-sized businesses that need detailed accounting, inventory tracking, and advanced reporting. Compared to lighter tools like Wave or Xero, Sage 50 leans more toward businesses with complex needs.

G2 Rating: 3.9/5

Sage 50 dashboard

Key Features

• Bank feeds & reconciliation for automated transaction imports.

• Invoicing & payments with customizable forms, quotes, sales orders, and online payment options.

• Inventory management with multi-level pricing, purchase orders, and real-time tracking.

• Financial reporting covering profit & loss, balance sheets, and advanced job costing.

• Payroll & HR modules for employee payments and tax compliance.

• Multi-company support for consolidating accounts across entities.

• Hybrid access with desktop reliability and optional cloud connectivity.

Pricing

Sage 50 offers annual subscriptions. The pricing is based on per user and starts from $668/year to $1,994/year. 

Add-ons like payroll and Sage HR come at an extra cost. A free 30-day trial is available.

Sage 50 pricing plans

Who Should Use It

Sage 50 is best for businesses that manage complex inventory, multiple companies, or need in-depth financial reporting. It suits experienced bookkeepers who prefer desktop software with cloud access. 

6. Zoho Books

Zoho Books is part of the larger Zoho ecosystem, which means if you’re already using Zoho CRM, Zoho Projects, or Zoho Payroll, this accounting tool plugs right in. It’s also one of the few tools that feels equally friendly to non-accountants while still being accurate enough for a CPA to trust. If you’re running e-commerce or service-based work and want real-time tracking without QuickBooks’ price tag, Zoho Books often becomes the go-to.

Zoho Books is currently rated 4.5 out of 5 on G2.

Zoho Books dashboard

Pricing

There’s a free plan for small businesses, and then paid plans start at $20/month (Standard). The Professional plan at $50/month adds inventory and vendor management, while the Premium plan at $70/month adds budgeting and advanced forecasting. 

If you pay annually, you get almost 25% discount on your annual billing.  

Zoho Books pricing plans

Who Should (and Shouldn’t) Use It

Zoho Books is ideal if you’re a freelancer growing into a small team, an e-commerce shop that needs inventory tracking, or a service business that bills projects and wants clean reporting without paying QuickBooks prices. On the other hand, if your business is very simple (say, a side hustle with a few invoices a month), Wave is easier and free. And if you’re a larger company with complex payroll or lots of integrations, QuickBooks or Xero might scale better.

Final Thoughts

Bookkeeping doesn’t have to be complicated, but it does have to be consistent. Bookkeeping software can turn messy spreadsheets into clarity and give you space to focus on the work that matters most.

At the end of the day, the “best” bookkeeping software is the one you’ll actually use or the one that frees you from having to use it at all.