The Best Accounting Software for Small Businesses: Our Top Five Picks

Starting your journey as a small business owner is an exciting adventure, but it can also feel a bit daunting. One of the most overwhelming aspects is choosing the right accounting software to keep your finances in order. With so many tools available online and countless reviews to sift through, it's easy to get lost. At Third Mesa, we’ve tested the top platforms and curated our favorites to help you simplify bookkeeping, save time, and set your business up for success.

Why Bookkeeping Software Matters

At the heart of every successful business lies accurate record-keeping. Whether you’re tracking expenses, managing payroll, or filing taxes, reliable bookkeeping tools for small businesses are essential.

While dozens of providers market themselves as small-business-friendly, not all are created equal. We recommend sticking with established, cloud-based platforms that balance ease of use, affordability, and scalability.

Let's dive into some of our top recommendations that can streamline your accounting processes and set you up for success!

1) QuickBooks Online: Our #1 Recommendation

For most of our clients, QuickBooks Online (QBO) is the best accounting software for small businesses. Our team uses it daily and appreciates its flexibility, innovation, and integrations.

Why We Love QBO:

• Thousands of integrations: QBO connects with a wide range of third-party apps so that you can customize it for your specific industry and enhance your business operations

• Scalability: Whether you’re a solopreneur or a growing company, QuickBooks adapts to your needs.

• Comprehensive features: Built-in payroll, payment processing, bill pay, and sales tax management.

• Constant innovation: Intuit invests heavily in AI tool development, training resources, and security upgrades.

The only downside? Pricing. QBO is slightly more expensive than some competitors, but we believe the value more than outweighs the cost. The ongoing resources allocated to AI tool development, security enhancements, and complimentary training materials equate to a premium service experience.

Ready to get started with QuickBooks Online? Check out our top five tips!

2) Xero: A Strong Alternative

If QuickBooks feels too complex for your current accounting needs, Xero is another excellent alternative. Many small business owners love its simple, user-friendly interface and affordability.

Key Features of Xero:

• User-friendly interface that’s perfect for beginners.

• Unlimited users—ideal for collaborative or in-house teams.

• Automation features such as bank feeds and integrations.

• Payroll through Gusto: While it doesn’t have built-in payroll, it integrates seamlessly with this popular payroll provider.

Xero is best suited for businesses that don’t need advanced reporting or analytics but want solid, easy-to-use accounting software.

3) Gusto Payroll: Stress-Free Payroll & HR

One of the more challenging roles for small business owners is managing payroll and HR tasks. Whether you have just one employee or a team of fifty, the learning curve can be steep. To simplify this process, we recommend Gusto Payroll as our preferred payroll provider.

Why Gusto Stands Out:

• Integrates seamlessly with both QuickBooks Online and Xero.

• Affordable pricing: Plans start at $49/month, with no setup fees.

• Unlimited payroll runs: No extra charges for running payroll multiple times.

• Benefits administration: Helps small businesses offer healthcare, retirement, and more.

• Tax compliance: Handles W-2s, 1099s, and state filings automatically.

While Gusto works beautifully for small to mid-sized businesses, we do find that as companies evolve, they may eventually transition to larger systems, such as ADP. But for most small businesses, Gusto is more than enough.

4) Melio: Simplify Bill Pay

Another crucial aspect of running any business is managing accounts payable. Every small business faces the reality of bills and payments that need timely attention, and navigating this can be daunting, especially with the rising prevalence of online payments and emailed invoices. For this, we recommend Melio as an exceptional platform to help you manage bills and payments efficiently.

Melio helps you:

• Automate bill capture and approvals.

• Pay vendors by ACH or credit card (even if they only accept checks).

• Track payments from a simple, easy-to-use dashboard.

• Stay organized and avoid missed or late payments.

5) Square: Streamline Payments

When it comes to running a business, this could be one of the most important decisions you make. Streamlining the process of receiving payments is crucial for maintaining a healthy cash flow and providing a seamless, positive experience for your customers.

With many business owners adopting hybrid models (online and in-person), you need a flexible and efficient platform. For this, we recommend Square.

Square’s Main Features

• App marketplace integrations: Connect with major platforms through the Square App Marketplace.

• Ease of use and quick setup: Get started with minimal tech experience.

• Customer loyalty programs to keep repeat buyers engaged.

• Industry-specific plan options designed for retail, restaurants, and service-based businesses.

• Free POS plan for businesses just getting started.

While Square is a reliable and accessible payment processor, it’s worth noting that processing fees can add up—and it’s not ideal if you need built-in payroll or scheduling tools. Businesses with international customers might consider Stripe, which supports over 135 currencies.

Still, we’ve seen many small business owners successfully utilize Square to simplify payments and enhance their customer experience.

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The Best Accounting Software is the One That Works for Your Business

Embarking on the adventure of small business ownership brings its own set of challenges. Still, with the right accounting and bookkeeping tools, you can save time, reduce stress, and make smarter financial decisions.

At Third Mesa, we help entrepreneurs and small business owners discover the systems that make their lives easier. Whether you choose these recommended tools or others, the important thing is to start with a system that works for you.

Want expert help setting up QuickBooks Online for your small business? Contact us today to schedule a consultation.