Choosing bookkeeping software: what every small business owner should know

When choosing bookkeeping software, you should select a digital tool that allows you to record, organize, and monitor your business’s financial transactions. Ideally, it should cover basic features like invoicing, inventory management, expense tracking, and reporting. 

In 2025, does your D2C company or consumer brand still rely on spreadsheets and manual journals? It is a high-risk approach!  According to recent data, about 64.4% of small business owners now use accounting software to manage their finances. Yet many still struggle! Why? Because they haven’t picked the right bookkeeping software for their business.

If you are searching for the best bookkeeping software for a small business, this article offers some good recommendations. You will also learn how to choose the right bookkeeping software for your business​, along with some proven tips. 

How to Choose the Right Bookkeeping Software for Your Business?

Choosing bookkeeping software is one of the most important financial decisions for any small business. The right platform keeps your books 100% accurate + makes you legally compliant. But with so many options out there, finding the best bookkeeping software for small business use can feel confusing! 

Below are seven key things you should consider before making a decision:

1. Go for Simple, Not Complicated

When choosing bookkeeping software, simplicity matters more than anything else! As a small business owner, you shouldn’t need accounting expertise to use your software. Thus, look for an easy-to-understand interface where you can quickly find what you need, such as invoices, expenses, and reports.

The best bookkeeping software for small business users usually offers:

• Tutorials
• Chat support
• Help centers (that explain every feature in plain language).

A simple dashboard also helps you avoid errors + saves you from wasting time figuring out complex settings. As a VP or director of a D2C company, your goal is to make bookkeeping a regular habit and not a stressful task.

2. Focus on What You Actually Need

Before buying, check if the software includes all the tools your business truly needs. Usually, it should cover:

• Creating invoices
• Tracking payments
• Managing expenses
• Filing taxes

The right solution should handle these core tasks easily. Furthermore, if you deal with inventory or GST/VAT, make sure those options are included too. Also, check if the software can connect directly with your bank account to record transactions automatically.

3. Choose Software That Can Grow With You

Your consumer brand today might be small, but it won’t stay that way forever! Choose bookkeeping software that grows with you instead of forcing you to switch later. Scalable software lets you:

• Add more users
• Handle more transactions
• Expand your financial reports (as your business gets bigger).

Additionally, look for systems that allow customization, such as personalizing invoices, setting different roles for team members, or adding new features later. The best bookkeeping software for small business owners usually offers flexible plans that you can upgrade as your needs increase. This way, you invest once and keep building on it as your company evolves!

4. Know What You’re Paying For

Before you select, take time to understand its pricing model. Most small business bookkeeping software offers multiple plans based on:

• Features
• User limits
• Storage capacity

Start by listing what your business truly needs and compare it with what each plan includes. Avoid paying extra for tools you’ll never use, but don’t go for the cheapest option if it limits your growth later. Ideally, you should look for software that provides a balance between affordability and functionality. 

Furthermore, some platforms also offer monthly and yearly payment options. So, choose the one that fits your cash flow. The goal is to get long-term value, not just a low upfront price!

5. Make Sure It Works With Your Other Tools

When choosing bookkeeping software, check how easily it connects with tools you already use, such as your:

• CRM
• E-commerce store
• Payment gateway
• Payroll system

Integration allows data to flow automatically between systems, which reduces manual entry and errors. This allows you to track revenue + expenses in real time.

6. Look for Reliable Support and Training

Even the best bookkeeping software for small business owners can feel complex at first! That’s why strong customer support and training materials are highly important. Thus, choose software that offers:

• Step-by-step guides
• FAQs
• Tutorials (that help you understand every feature).

Also, check if there’s real-time support through chat, email, or phone, for when you face technical problems!

7. Protect Your Financial Data

Security should be a top priority when choosing bookkeeping software. Your financial data includes sensitive details about your business, customers, and vendors. Thus, it must stay protected.

As a VP or director of a growing D2C company operating in multiple regions like the US, UK, and Australia, you should look for software that uses:

• Encrypted connections
• Secure cloud storage
• Backup systems that save your data automatically.

Also, check for features like two-factor authentication and user permission controls, which prevent unauthorized access. If your data is stored on the cloud, confirm that the provider follows recognized data protection standards.

3 Tips for Making the Right Selection

Did you know that about 71% of small business owners already use accounting software or apps to manage their finances? Yes, and that means many D2C companies and consumer brands recognize how important the right bookkeeping software is. 

If you’re still deciding on the best bookkeeping software, follow the tips below:

Best Bookkeeping Software for Small Businesses in 2025

Choosing the best bookkeeping software for small business owners can make a big difference in managing daily finances. The right software simplifies tasks like:

• Income tracking
• Expense management
• Invoicing
• Financial reporting

Some startups may prefer free tools like Wave, while growing D2C companies may need advanced platforms like QuickBooks Online, Xero, or Zoho Books. To pick the right product, below is a list of the best bookkeeping software for small businesses​, you may pick in 2025:

Bookkeeping Software = Hidden Costs! Hire Atidiv to Achieve Up to 60% Cost Savings in 2025!

So now you know how to pick the best right bookkeeping software that can organize your business finance + keep you compliant. But most platforms come with hidden costs that many small business owners overlook! These include:

• Upgrade fees for advanced features
• Charges for adding users
• Additional expenses for integrations and technical support

On top of that, you still need a dedicated staff member or accountant to manage the system, which adds to operational costs. That’s why in 2025, many D2C companies are now hiring accounting companies in the USA, like Atidiv. 

Our expert team at Atidiv has over 16 years of experience in managing end-to-end finance and accounting for businesses at every stage. With us you get:

Recently, Atidiv partnered with a growing NYC start-up and delivered 80% time savings, 50% cost reduction, and 99% accuracy. Want to enjoy similar benefits? Book a free consultation call to learn how we can help you!

Choosing Bookkeeping Software FAQs

1. How do I know which bookkeeping software is best for my small business?

Start by listing your needs, like invoicing, expense tracking, and payroll. Then compare options based on features, pricing, and scalability. It is recommended that you choose software that fits your business size and growth plans, not just the cheapest plan available. Free trials can also help you test before committing.

2. What hidden costs should I watch out for when buying bookkeeping software?

Many tools charge extra for:

• Advanced features
• Additional users
• Storage
• Integrations with apps like payroll or CRM

Some also increase prices after the first year! So, always read the pricing terms carefully to avoid unexpected expenses later.

3. Do I still need a bookkeeper if I use accounting software?

Yes! Software automates calculations and reports. But you still need someone to:

• Interpret data
• Reconcile accounts
• Ensure compliance

A skilled bookkeeper helps you make sense of numbers + avoid costly financial mistakes.

4. What’s new in bookkeeping software trends in 2025?

In 2025, small businesses are adopting AI-based bookkeeping tools that:

• Automate data entry
• Detect errors
• Provide real-time insights

However, many owners are also outsourcing bookkeeping to accounting companies in the USA to combine automation with expert oversight for greater accuracy and cost savings.

5. Is cloud-based bookkeeping software safe for my financial data?

Yes! To pick the right provider, you should look for features like:

• Encryption
• Two-factor authentication
• Regular backups

Reputable platforms follow strict data security standards to protect sensitive business information stored in the cloud.