10 Best Bookkeeping Software for Small Businesses

Keeping track of income, expenses, and financial records is one of the toughest challenges small business owners face. Manual bookkeeping or relying on outdated spreadsheets often leads to errors, wasted time, and unnecessary stress, all while taking focus away from running the business.

That’s where modern bookkeeping software comes in. The right tool can simplify financial management, automate repetitive tasks, and give you real-time insights into your cash flow. For small businesses, this can mean better decision-making, improved compliance, and more time to focus on growth.

In this blog, we’ll highlight the 10 best bookkeeping software options for small businesses in 2025. You’ll discover their key features, pricing, and what makes each one a top choice, helping you decide which solution fits your business needs best.

What are the Factors to Consider When Choosing Bookkeeping Software?

The right bookkeeping software can save time, reduce errors, and keep your business compliant, but not every tool will suit your needs. Before making a decision, evaluate the following factors:

• Ease of Use – Is the software intuitive enough for non-accountants, or does it require advanced expertise?
• Automation – Look for features like automated invoicing, bank reconciliation, and expense categorisation.
• Integrations – Ensure it connects with your existing tools (e.g., payroll, CRM, or e-commerce platforms).
• Compliance – Especially in the UK, check support for HMRC’s Making Tax Digital (MTD) and VAT submissions.
• Scalability – Can it grow with your business as you add more users, clients, or complexity?
• Pricing & Value – Compare subscription tiers to see if you’re getting the right features for your budget.
• Customer Support – Reliable, responsive support (live chat, phone, or email) can make a big difference.

What are the 10 Best Bookkeeping Software for Small Businesses?

Let’s dive into the top bookkeeping solutions available today. Each option has its own strengths and weaknesses, making it easier for you to find the one that fits your business needs. Here are the tools:

1. QuickBooks - Best for Deep Financial Insights

QuickBooks is a powerhouse in the world of accounting, offering deep financial insights perfect for small to medium-sized enterprises. This accounting system is specifically designed for businesses that require detailed and advanced operational control. If you need to understand your company's financial health with precision, QuickBooks provides tools like cash flow projections and in-depth reporting.

Curious about whether it’s time to move from QuickBooks to Sage Intacct? Check out our guide: QuickBooks to Sage Intacct: Is it Time to Convert?

Why Should You Pick This Software?

• Customizable reports and templates for tailored insights
• Dashboard personalization to highlight critical data
• Automatic error detection in financial reports
• Strong compliance support for MTD and income tax

Why Should You Not Pick This Software?

• Steeper learning curve compared to beginner-friendly tools
• No built-in time tracking (requires paid add-on)

Pricing Plans

• Simple Start – $19/month: For 1 user, covers basics like income & expense tracking, invoicing, tax deductions, and reports.
• Essentials – $37.50/month: For up to 3 users, adds bill management, recurring invoices, and time tracking.
• Plus – $57.50/month: For up to 5 users, includes project tracking, inventory management, and budgeting tools.
• Advanced – $137.50/month: For up to 25 users, adds custom reporting, advanced analytics, workflow automation, and dedicated support.

2. Xero - Best for Integrations

Xero is a cloud-based accounting software platform designed for small and growing businesses. It offers real-time financial insights, automates key tasks like invoicing and bank reconciliation.

Why Should You Pick This Software?

• Secure client portal for collaboration
• Asset depreciation tracking and advanced finance tools
• Over 1,000 integrations with third-party apps
• Online payments through invoicing

Why Should You Not Pick This Software?

• Desktop interface feels outdated
• Less beginner-friendly than rivals

Pricing Plans

• Starter – $29/month: Includes sending up to 20 invoices and quotes, entering 5 bills, reconciling bank transactions, capturing bills/receipts with Hubdoc, and viewing short-term cash flow snapshots.
• Standard – $46/month: Covers everything in Starter plus unlimited invoices and bills, bulk transaction reconciliation, and short-term cash flow snapshots.
• Premium – $69/month: Includes all Standard features, with additional benefits like multi-currency support and more advanced financial management tools.

For additional reading: Xero to Sage Intacct: Migration Made Easy

3. Sage Intacct – Best for AI-Based Accounting

Sage Intacct Business Cloud Accounting is an excellent choice for businesses looking to establish a strong brand identity while managing their finances. It is trusted for its robust reporting and automation capabilities and for offering enhanced visibility into financial performance.

For a deeper understanding of how Sage Intacct can transform your SaaS or software business, explore our Ultimate Guide: Sage Intacct for SaaS & Software Companies

Why Should You Pick This Software?

• Customizable invoices, reports, and branding
• Modern invoicing and quoting workflows
• Strong reporting with tailored profit and loss views
• Seamless integration with other Sage products

Why Should You Not Pick This Software?

• No automation for payment reminders
• Lacks bulk import for expenses or contacts

Pricing Plans

Pricing details are not available to the public. One needs to request pricing from the sales team.

4. FreeAgent – Top Choice for Freelancers and Contractors

If you're a freelancer, sole trader, or contractor, FreeAgent is designed with you in mind. It is a simple bookkeeping software for small business that strikes a great balance between providing powerful features and maintaining a simple, user-friendly interface.

Why Should You Pick This Software?

• Tax timeline and scenario prediction tools
• Cash flow alerts for financial health
• Clear invoicing timeline to track payments
• Free for NatWest business account holders

Why Should You Not Pick This Software?

• Some unclear terminology and tricky navigation
• Invoice uploads require an add-on

Pricing Plans

• Monthly Plan: $11/month (50% off for the first six months, originally $22/month). Includes Sales Tax Reporting & Multi-Currency invoicing. Optional add-ons available within your FreeAgent account and may incur additional charges.
• Annual Plan: $110/year (50% off for the first year, originally $220/year; equivalent to $9.17/month). Includes Sales Tax Reporting & Multi-Currency invoicing. Optional add-ons available within your FreeAgent account and may incur additional charges.

5. NetSuite – Best for Automation

NetSuite Cloud Accounting Software is a leading cloud-based financial management solution designed for businesses of all sizes. As part of Oracle’s NetSuite ERP suite, it offers a unified platform that streamlines accounting, compliance, and reporting processes.

For a deeper dive into how NetSuite can transform your business operations, explore our comprehensive guide: Understanding NetSuite: A Beginner's Guide

Why Should You Pick This Software?

• Automates invoicing, tax compliance, and reconciliations
• Advanced analytics and performance reporting
• Multi-currency and multi-subsidiary support
• Scales into ERP with modules like CRM and e-commerce

Why Should You Not Pick This Software?

• Steep learning curve for smaller teams
• Costly and time-intensive implementation

Pricing Plans

Pricing details are not available to the public. One needs to request pricing from the sales team.

6. FreshBooks – Ideal for Service-Based Businesses

FreshBooks is designed for service-based businesses, freelancers, and sole traders who need simple yet powerful software at a fair price. Its standout feature is its intuitive and refreshingly easy-to-use interface.

Why Should You Pick This Software?

• Precise time tracking for billable hours
• Easy conversion of hours into invoices
• Supports online payments and client management
• 24/7 chatbot support for peace of mind

Why Should You Not Pick This Software?

• Limited advanced budgeting and forecasting
• No client portal like Xero
• Some quirks with currency settings

Pricing Plans

• Lite ($6.30/mo, 70% off for 3 months) – Send invoices to 5 clients, track expenses in real time, create/send estimates, get paid via credit cards & ACH, and generate tax-time reports.
• Plus ($11.40/mo, 70% off for 3 months, Most Popular) – Send invoices to 50 clients, track expenses in real time, create estimates/proposals/retainers, accept credit cards & ACH payments, generate tax reports, and run financial/accounting reports.
• Premium ($19.50/mo, 70% off for 3 months) – Send invoices to unlimited clients, includes all Plus features, plus full financial and accounting reports.
• Select (Custom Pricing) – Send invoices to unlimited clients, includes all Premium features, plus lower credit card transaction fees and capped ACH fees, with personalized consultation.

7. Crunch – Best All-In-One Solution for Small UK Businesses

Crunch offers a unique proposition by combining free accounting software with optional, paid accountancy services. This all-in-one approach is perfect for small business owners who want the convenience of software with the option to get expert advice when needed.

Why Should You Pick This Software?

• Start with free software and add services as needed
• Access to professional accountants via live chat
• Flexible tax filing support for growing businesses

Why Should You Not Pick This Software?

• Less feature-rich than advanced competitors
• Primarily suited for sole traders and very small businesses

Pricing Plans

• Sole Trader Pro (£21.60 +VAT/month, promo code 20FOR6) – All-in-one support for the self-employed, including expert help, tools, and tax filings. Option to save £64.80 with annual plan.
• Limited Company Pro (£72 +VAT/month, promo code 20FOR6) – Core tools and support to help limited companies stay compliant and manage business operations. Option to save £216.00 with annual plan.
• Limited Company Premium (£109.60 +VAT/month, promo code 20FOR6) – Full support for limited companies, including Self Assessment, tax-saving advice, and extra peace of mind. Option to save £328.80 with annual plan.

8. IRIS KashFlow – Best for Customisable Reporting

IRIS KashFlow Bookkeeping is a cloud-based bookkeeping tool made for small businesses and sole traders in the UK. It offers an easy way to manage income, expenses, invoices, receipts, and core financial tasks via the cloud, so users can work from anywhere.

Why Should You Pick This Software?

• Built-in compliance with UK tax regulations (e.g., MTD, CIS)
• Bank linking via Open Banking
• Recurring invoices and online payments
• Collaboration via KashFlow Connect

Why Should You Not Pick This Software?

• Limited relevance outside the UK
• It may be too advanced or costly for very small firms

Pricing Plans

• Starter (£1.25/month, 90% off for 6 months) – Ideal for sole traders, contractors, and small businesses. Includes unlimited quotes, 10 invoices, up to 25 bank transactions, single-user access, VAT management, bank feeds, and faster payments via KashFlow.
• Business (£2.55/month, 90% off for 6 months, Recommended) – Ideal for growing businesses and limited companies. Includes unlimited quotes & invoices, unlimited bank transactions, multi-user access, VAT management, bank feeds, and faster payments via KashFlow.

9. Ember – Best for Quick Onboarding

Ember is a cloud-based tax and bookkeeping solution built for small businesses and freelancers in the UK. It combines intuitive software with real accountant support, helping users stay on top of bookkeeping, tax filings, and compliance.

Why Should You Pick This Software?

• Automates transaction categorisation and tax tracking
• Direct VAT, payroll, and corporation tax filing
• Real-time financial insights and deadline reminders
• Human accountant support included

Why Should You Not Pick This Software?

• UK-only focus limits global use
• Subscription cost may be high for very small firms

Pricing Plans

Pricing details are not available to the public.

10. Clear Books – Best for Local UK Support

Clear Books is a UK-based simple bookkeeping software for small businesses. One of its greatest strengths is its commitment to providing excellent, accessible support. If you value being able to get help from a local support team, Clear Books is a worthy contender.

Why Should You Pick This Software?

• Strong MTD compliance and tax projection tools
• Simple invoicing, quotes, and project creation
• Helpful search and navigation features
• Responsive phone support from UK-based team

Why Should You Not Pick This Software?

• Onboarding can be frustrating
• Some folder naming conventions are confusing

Pricing Plans

• MTD Income Tax (Free) – For self-employed sole traders and landlords with basic needs. Includes: MTD Income Tax quarterly updates, year-end filing (coming soon), income/expenses recording, and bank feeds.
• Small (£7.50/mo for 3 months, then £15/mo) – For limited companies, sole traders, landlords, partnerships, and charities. Includes everything in Free, plus: sales & purchases tracking, custom invoices, quotes & estimates, contact list, reporting suite, and customer statements.
• Medium (£15.50/mo for 3 months, then £31/mo) – For limited companies, sole traders, landlords, partnerships, and charities. Includes everything in Small, plus: MTD VAT submissions, purchase orders & approvals, CIS reporting (construction), and unlimited budgets.
• Large (£20.50/mo for 3 months, then £41/mo) – For limited companies, sole traders, landlords, partnerships, and charities. Includes everything in Medium, plus: project accounting, project-specific invoice templates, configurable project reports vs budgets, multi-currency, and employee expense claims.

Accountancy Cloud: Expertise Beyond Accounting Platforms

Choosing the right bookkeeping software is only the first step in taking control of your finances. While tools can streamline admin and keep you compliant, true financial clarity comes from having the right partner by your side. That’s where Accountancy Cloud steps in. By combining expert bookkeeping, payroll, tax services, and on-demand CFO support, we go beyond software to give your business the strategic edge it needs.

If you’re ready to save time, scale faster, and make smarter decisions, partner with us and turn your finances into a growth engine. Get in touch with us today.

Next Steps: Turn Bookkeeping into a Strategic Advantage

Choosing the right bookkeeping software can transform how a small business manages finances. From automating tasks and ensuring compliance to providing real-time insights, the right tool saves time, reduces errors, and supports growth.

By aligning your choice with your business size, complexity, and budget, you can streamline operations and make smarter financial decisions, turning bookkeeping from a chore into a strategic advantage.

Frequently Asked Questions

Is online bookkeeping software safe for small businesses in the UK?

Yes, reputable online accounting software is very safe. Providers use high-level security measures like data encryption and secure cloud servers to protect your financial information.

Can bookkeeping software automate key financial tasks?

Absolutely. Automation is a primary benefit offered by most small business accounting bookkeeping software. Your accounting system can automate tasks like invoicing, bank reconciliation, expense categorisation, and even preparing reports for tax digital submissions.

Are there free small business bookkeeping software?

Yes, several providers offer a free version of their bookkeeping software. Options like Zoho Books and Crunch provide excellent free plans that are perfect for a new small business owner or sole trader. While they may have limitations, they offer a great way to start.

How do QuickBooks, Xero, and Sage compare for UK small businesses?

QuickBooks is user-friendly, Xero excels in cloud flexibility, and Sage offers strong compliance and payroll features. The right choice depends on your business size, budget, and reporting needs.

What support or customer service options do major bookkeeping software providers offer?

Most providers offer live chat, email, phone support, and extensive help centres. Some also provide 24/7 assistance, dedicated account managers, or community forums, depending on the pricing plan.

What features should I look for in bookkeeping software for my small business?

Look for bookkeeping software that is user-friendly, supports invoicing, expense tracking, bank reconciliation, and basic reporting. Ideally, they should also be scalable.

Can bookkeeping software help automate key financial tasks for small businesses?

Yes, bookkeeping software can automate invoicing, expense categorization, payroll calculations, and financial reporting, saving time and reducing errors for small businesses.