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5 Best Accounting Software Packages for Small Businesses in 2025

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For accounting firms that cater to small businesses, the symbiosis between the firm and its clients is paramount. The chosen accounting software can significantly influence this relationship, impacting everything from daily operations to strategic financial planning. In today's fast-paced business environment, the right software can facilitate seamless integration between a small business and its accounting firm, enhancing collaboration, improving accuracy, and driving efficiency. Here's a look at top accounting software options that foster strong connections between small businesses and their accounting partners.

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Software Best For Key Features Collaboration & Integrations Ideal For Firms
QuickBooks Online Small businesses seeking automation and scalability AI-powered late payment reminders, personalized invoices, and expense report automation. Integrates with Shopify for order and payout imports. Hundreds of third-party integrations, including Shopify Scalable solution for growing firms managing multiple clients
Xero Small businesses and startups Onboarding specialists (first 90 days), minimalist design, W-9 and 1099 management, short-term cash flow tracking Seamless Shopify integration, third-party app support Ideal for startups and small firms needing ease of use
FreshBooks Service-based businesses Invoicing, expense and income tracking, automated emails, and profit projections Limited inventory management, collaborators at extra cost Best for service-based firms with basic accounting needs
Wave Cost-conscious small businesses Free plan with unlimited invoices, bookkeeping records, and online payments. Pro plan offers auto-imported bank transactions and receipt capture No Shopify integration, limited third-party integrations Great for small firms or startups on a budget
Zoho Books New or budget-conscious businesses Free version for companies with <$50K annual revenue, mobile app, inventory tracking, auto-completion of bookkeeping tasks Integrates with PayPal, Stripe, and Shopify (via Flow, with additional cost) Efficient for firms working with Zoho ecosystem clients

 

QuickBooks Online

QuickBooks Online stands out for its ubiquity and familiarity among accounting professionals. Its comprehensive features support a wide range of business activities, from invoicing and payroll to advanced reporting.

For accounting firms, QuickBooks offers collaborative tools like simultaneous access to financials, real-time updates, and easy sharing of reports and documents. Its extensive ecosystem of add-ons and integrations means that both small businesses and accounting firms can tailor the experience to their needs, ensuring a cohesive financial management process.

whats-the-best-accounting-software-for-small-businesses-Quickbooks-Online

Pros:

  • Includes automated late payment reminders, personalized invoices, and expense report automation by extracting details from photos or emails.

  • User-friendly dashboard with core features like cash flow view, invoice generation, and bookkeeping automation.

  • Supports hundreds of third-party integrations, including Shopify, which automatically imports orders and payouts.

  • Offers inventory tools and billable hours tracking in higher-tier plans, making it suitable for growing businesses.

Cons:

  • Features like multiple currency transactions and billable hours are only available in higher-tier plans.

  • Inventory tools are restricted to the Plus and Advanced packages.

  • Despite its simplicity, new users may still need some time to become familiar with the system.




 

Xero

Xero’s cloud-based platform is a haven for firms looking for real-time financial data and insights.

The unlimited user model allows both small business teams and their accounting partners to access financial data anytime, anywhere, fostering a transparent and inclusive approach to financial management.

whats-the-best-accounting-software-for-small-businesses-Xero

Pros: 

  • Minimalist design makes it easy for small business owners and startups to use without accounting expertise.

  • Provides access to onboarding specialists during the first 90 days to assist with setup.

  • Seamlessly integrates with Shopify, simplifying e-commerce accounting.

  • Includes W-9 and 1099 management, short-term cash flow tracking, and business snapshots. 

Cons: 

  • Bulk expense tracking is only available in higher-tier plans

  • Essential accounting functions are included, but more advanced features require upgrading.

  • Compared to QuickBooks, Xero’s reporting capabilities may be less comprehensive for larger firms.



 

 

FreshBooks

FreshBooks is designed with service providers in mind, offering intuitive invoicing, time tracking, and project management tools. For accounting firms, FreshBooks makes it easy to collaborate with clients on financial management.

The software's emphasis on client interactions, such as simplified billing and payments, ensures that firms can offer a more personalized, service-focused experience to their clients, enhancing client satisfaction and retention.

whats-the-best-accounting-software-for-small-businesses-Freshbooks

Pros:

  • Designed for simplicity, making it ideal for freelancers and service-based businesses.

  • Includes automated emails (late payment reminders, successful payment confirmations) and profit projections.

  • Covers invoicing, expense tracking, and income management.

  • Higher-tier plans offer more automation and lower credit card transaction fees.

Cons: 

  • Entry-level plans cap the number of billable clients at five, making it less
    suitable for firms with larger client bases.

  • Adding collaborators incurs additional fees, increasing the total expense.

  • Less sophisticated inventory tracking compared to other platforms,
    making it better suited for service-based businesses rather than e-commerce.

 

 

Wave

Wave provides a free, straightforward accounting solution for small businesses, making it an ideal choice for startups and small enterprises with tight budgets.

For accounting firms, Wave offers the basic tools needed to manage accounting and invoicing for their clients without additional software costs. This can be particularly appealing for firms serving clients who are just starting out or those with straightforward financial management needs.

whats-the-best-accounting-software-for-small-businesses-wave

Pros:  

  • Includes unlimited invoices, bookkeeping, and online payments—ideal
    for startups and small businesses.

  •  Auto-imports bank transactions, merges and categorizes them, and automates late payment reminders.

  • Digitally captures and organizes receipts, reducing manual data entry.

  • Intuitive design suitable for non-accountants.

Cons: 

  • Lacks direct Shopify integration, limiting its e-commerce appeal.

  • Fewer integrations compared to competitors
    like QuickBooks and Xero.

  • The free version offers essential tools but lacks advanced reporting and inventory management.



 

Zoho Books

For small businesses already leveraging the Zoho ecosystem, Zoho Books offers an integrated accounting solution that seamlessly syncs with other Zoho apps.

Accounting firms working with such clients can benefit from the streamlined data flow between Zoho applications, making it easier to manage finances, customer relationships, and inventory in a unified platform. This integration facilitates a more holistic approach to business management, allowing firms to provide comprehensive advisory services.

whats-the-best-accounting-software-for-small-businesses-Zoho-books

Pros:  

  • Available for companies earning less than $50,000 in annual revenue, making it highly budget-friendly.

  • Mobile-friendly platform allows business owners to manage finances on the go.

  • Syncs seamlessly with other Zoho apps, streamlining business operations.

  • Includes built-in inventory management, making it suitable for product-based businesses.

Cons: 

  • Only available for businesses earning less than $50,000 annually, limiting its accessibility.

  • Shopify integration requires using Zoho Flow, which incurs an additional monthly fee.

  • While suitable for small businesses, larger firms may find it lacks the robust reporting and automation of QuickBooks or Xero.

 

 

How to Choose the Right Accounting Software

 

Define Your Business Needs

Before choosing a platform, consider your business type, size, and accounting needs. Service-based businesses should prioritize invoicing and project management (FreshBooks). Product-based companies need inventory tracking (QuickBooks, Zoho Books). Freelancers should focus on simplicity and affordability (Wave, FreshBooks). Growing SMBs or firms require scalability, multi-user access, and advanced reporting (QuickBooks Online, Xero).

Consider Integration Capabilities

Your accounting software should integrate with your existing tools, such as e-commerce platforms, CRMs, or payment gateways. E-commerce businesses need Shopify or Stripe integrations (QuickBooks, Xero). CRM-heavy companies benefit from native connections (Zoho CRM + Zoho Books). Automation-first firms should choose platforms with built-in or third-party automation (QuickBooks, Botkeeper) to reduce manual work.

Prioritize Cloud Accessibility and Collaboration

For small businesses working with accounting firms, cloud-based platforms are essential for real-time collaboration and data sharing. Remote teams or accounting partnerships will benefit from cloud platforms like Xero and QuickBooks, which allow both you and your accountant to access financial data simultaneously. 

If you need multi-user access, Xero offers unlimited user accounts, making it perfect for teams needing broad accessibility. For on-the-go management, platforms with robust mobile apps (like Zoho Books) make it easier to manage finances remotely.

Evaluate Usability and Learning Curve

Accounting software should simplify finances, not complicate them. User-friendly platforms like FreshBooks and Wave are easy for non-accountants. Feature-rich options like QuickBooks and Xero offer advanced tools but may require more training. Xero’s 90-day specialist support helps new users onboard smoothly.

Plan for Scalability

As your business grows, choose software that scales with you. Tiered platforms like QuickBooks and Xero offer advanced tools for expanding companies. Startups can start with cost-effective options like Wave or Zoho Books and upgrade later. 

Prioritize Security and Compliance

Your accounting software should be able to protect sensitive data. Cloud platforms like Xero, QuickBooks, and Zoho Books offer bank-level encryption. Choose software with permission controls and support for multi-currency transactions and tax compliance if you work internationally.

 

Building a Collaborative Future

Choosing the right accounting software is about more than just features; it's about finding a platform that supports a collaborative and transparent relationship between small businesses and their accounting firms. The ideal software should offer:

  • Ease of Use: Both clients and firms benefit from intuitive interfaces that reduce the learning curve and simplify financial management.

  • Accessibility: Cloud-based platforms ensure that financial data is accessible to both parties, anytime and anywhere, facilitating timely decisions and advice.

  • Integration: The ability to integrate with other business tools and systems streamlines operations and provides a more comprehensive view of the business.

  • Scalability: As small businesses grow, the software should be able to accommodate evolving needs without requiring a transition to a new platform.

  • Security: Protecting sensitive financial data is paramount, making robust security features a critical consideration for any software choice.

 

For users of QBO and Xero in particular, Botkeeper provides a platform that enables the transparent relationship and collaboration firms seek with their small business clients. Botkeeper takes on the tedious and time-consuming tasks your bookkeeper performs, reducing the amount of time your firm spends on accounting. It also saves you money and eliminates virtually all errors in your bookkeeping efforts. Basically, Botkeeper added to QBO or Xero makes a dream team of automation!

The relationship between small businesses and their accounting firms is significantly enhanced by the choice of accounting software. By selecting a platform that prioritizes collaboration, integration, and ease of use, accounting firms can provide exceptional service to their clients, laying the foundation for mutual growth and success.

To learn more about accounting and bookkeeping software, be sure to visit Botkeeper’s free, dedicated resource.

 

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