How to Choose the Best Ecommerce Bookkeeping Software for Your Online Store

As a savvy online business owner, you’re likely juggling inventory management, customer service, and marketing strategies all at once. 

But let’s face it: without solid financial tracking, even the most innovative product ideas can fall flat. Enter doola Bookkeeping! 

Right tools like these not only simplify your financial processes but also provide insights that empower you to make informed decisions for growth.

But with so many options available — from comprehensive platforms touting advanced features to simpler apps designed for ease — how do you choose? 

In this guide, we’ll walk you through everything you need to consider when selecting bookkeeping software tailored specifically for your e-commerce store.

Whether you’re just starting or looking to upgrade your current system, read on to discover how to streamline your finances and set yourself up for success in this competitive marketplace!

Key Features to Look for in Ecommerce Bookkeeping Software

When it comes to choosing the right bookkeeping software for your ecommerce store, you need to weigh all the options using multiple factors. 

To help you make an informed decision, here are some key features to look for in bookkeeping software specifically designed for ecommerce businesses:

1. Integration Capabilities

One essential feature to consider is whether your bookkeeping software supports seamless integration with all your financial accounts. 

This will allow for real-time syncing of sales data, expenses, taxes, and inventory levels without any manual input.

2. Multi-Currency Support

If you have customers from different countries or sell products in multiple currencies, you need bookkeeping software that supports multi-currency transactions. 

This will help you accurately record and track international sales without having to convert currencies manually.

3. Automatic Bank Reconciliation

Reconciling bank statements with books can be tedious but is crucial for accurate financial reporting. 

Invest in online bookkeeping software that offers automatic bank reconciliation. This feature compares your bank statement entries with those in the system and flags discrepancies, if any.

4. Tax Management

Ecommerce businesses have unique tax needs, such as collecting sales tax from customers across different states or countries. 

A good bookkeeping software should have built-in tax management capabilities that cater to the specific needs of an online business.

5. Reporting and Analytics

Insightful reports and analytics are essential for understanding the financial health of your ecommerce business. 

Look for software that offers customizable dashboards, real-time data visualization, and detailed financial reports to help you make informed decisions.

6. Invoicing Tools

As an ecommerce store owner, you’re likely to face delays in receiving customer payments, which can affect your cash flow.

That’s why you need bookkeeping software with advanced invoicing capabilities for better cash flow management.

By creating and sending professional invoices easily, you can get paid faster and improve cash flow while managing accounts payable and receivable to achieve the perfect balance.

7. Scalability

Your ecommerce business will grow over time, and it is crucial to choose a bookkeeping software that scales with your business needs. 

Make sure the software offers add-ons or integrates with other tools that can adapt to your expanding business.

Top 3 Bookkeeping Software for Ecommerce Stores in 2025

Choosing the right bookkeeping software depends on the specific needs and requirements of your ecommerce store. 

These top 3 options are highly recommended by industry experts and are expected to continue being popular choices in 2025 due to their innovative features and user-friendly interfaces. 

So, do thorough research and consider your business’s unique needs before making a decision.

1. doola Bookkeeping

First up, we have doola Bookkeeping, an all-in-one bookkeeping and accounting platform that has become a top choice due to its user-friendliness, affordable pricing plans, and advanced features.

In terms of features, it comes loaded with everything needed to streamline your finances and automate mundane bookkeeping tasks. 

It helps you create invoices, track income and expenses, reconcile bank accounts automatically for reconciliation, and generate monthly and yearly statements like profit and loss reports.

However, what gives us an edge over the competition is our team of experienced bookkeepers and CPAs, who work with you to ensure accuracy, efficiency, and confidentiality in all your books.

🏆 What’s It Best For?

doola Bookkeeping is the perfect software for ecommerce store owners who want to streamline their bookkeeping process and save time and effort. 

It is especially useful for newly established or medium-sized businesses that are looking for an affordable bookkeeping solution with advanced reporting and tax management features.

Our intuitive bookkeeping software is designed for entrepreneurs with limited time, resources, and patience. It allows them to navigate the system and find what they need quickly and easily.

It does not require any previous accounting knowledge or experience, making it ideal for new business owners who may not have a strong background in finance. 

How Does It Work?

doola Bookkeeping works by integrating with all your financial accounts and automatically syncing all your sales, expenses, taxes, refunds, and other transactions in real-time. 

This eliminates the need to manually input data, reducing errors and saving you hours of tedious bookkeeping work.

It also automates transaction categorization, which saves you time from manually categorizing every transaction and ensures accurate bookkeeping records.

The software also offers a user-friendly interface that is easy to navigate and understand, even for non-accountants. 

From one central dashboard, you can easily generate financial reports and track your business’s overall financial health.

Another crucial feature is its tax assistance.

Be tax-ready with the doola Bookkeeping year-end package so you can easily file taxes and avail yourself of deductions like travel, marketing, and equipment costs for extra savings.

How Much Does It Cost?

Our pricing plans start at $25/month for the bookkeeping software​​, and you can also avail additional bookkeeping and tax filing services for a fraction of the cost.

doola Bookkeeping is affordable and keeps its quality of service high. It offers excellent customer support through live chat, email, or phone during business hours.

Features:

✔️ Income and Expense Tracking

✔️ Business Metrics

✔️ Auto-Tagging Transactions

✔️ Dedicated Bookkeepers

✔️ Self-Serve Invoice Creation

✔️ Financial Statements

✔️ Tax Filings

✔️ Catch-up Bookkeeping

✔️ Tax-Ready Year-end Package for Tax Filing

2. Bench Accounting

Bench Accounting is cloud-based bookkeeping software specifically designed for small businesses and independent entrepreneurs. 

It streamlines the bookkeeping process by automating tasks, providing real-time financial updates, and offering personalized support from a team of in-house bookkeepers.

This easy-to-use bookkeeping platform reduces stress by providing accurate financial reports and personalized support from certified bookkeepers.

This sets it apart from other software by combining technology with human expertise. This saves both time and resources that can be better utilized in other areas of your business.

🏆 What’s It Best For?

Bench Accounting is best suited for small business owners and freelancers who want to streamline their bookkeeping process without hiring a full-time accountant. 

It is also great for those who do not have the time to manage their books or need an expert who can give their time and expertise to help them streamline finances and file taxes.

How Does It Work?

Bench Accounting works by connecting your bank accounts and credit card information to its software, allowing it to track your income and expenses in real time automatically. 

The software then categorizes these transactions into different accounts, such as sales, payroll, or supplies. This eliminates the need for manual data entry and minimizes human error.

Once all your transactions are categorized, Bench Accounting’s team of in-house bookkeepers reviews them to ensure accuracy before reconciling them with your financial statements. 

They also provide you with monthly reports that give you an overview of your finances, making it easier for you to make informed decisions about your business.

How Much Does It Cost?

Bench’s basic bookkeeping plan starts at $349/month, and its full-service bookkeeping plan starts at $699/month, which includes income tax advisory and filing.

Features:

✔️ Easy-to-use Platform

✔️ Personalized Support

✔️ Flexible Pricing Plans

✔️ Tax Preparation Assistance

✔️ Real-time Reporting

3. Bookkeeper360

Ecommerce software solutions like Bookkeeper360 have emerged to provide businesses with a comprehensive bookkeeping system. 

By combining simplicity and functionality, it provides a streamlined bookkeeping experience that gives you complete control over your financial status at any given moment. 

This means that all sales transactions, expenses, and other financial data are automatically imported into the software in real-time, eliminating the need for manual data entry. 

It helps business owners efficiently manage their finances, invoicing, and tax preparation by tracking financial transactions, reconciling bank accounts, and preparing monthly statements. 

Moreover, Bookkeeper360 has powerful financial reporting capabilities that allow for quick analysis of financial data.

🏆What’s It Best For?

Bookkeeper360 is primarily designed for small to medium-sized ecommerce businesses, offering integrations with popular ecommerce platforms like Shopify.

Its user-friendly interface and powerful features make it a suitable choice for startups and growing online stores. 

How Does It Work?

Bookkeeper360 operates on a cloud-based system that allows users to access their accounts from any device with an internet connection. 

After signing up for the software, users can connect their bank accounts and credit cards to synchronize all transactions automatically. 

They can also upload their receipts and invoices to keep track of expenses accurately.

The software uses double-entry bookkeeping principles to record all financial transactions accurately. 

Through the platform, users can create invoices, track sales and expenses, manage inventory levels, process payments, generate financial reports, and more.

How Much Does It Cost?

Bookkeeper360 offers flexible pricing plans starting at $399 per month. Or, you can opt for a more advanced Controller plan with all popular add-ons, starting at $1,149 per month.

The prices may vary depending on the size of your business but are generally affordable considering the comprehensive set of features offered by the software.

Features:

✔️ Advanced Reporting

✔️ Cashflow Analysis

✔️ Dedicated Accountant

✔️ Monthly or Weekly Accounting

✔️ Cash Basis or Accrual Basis

✔️ Monthly Financial Reports

Steps to Choose the Best Ecommerce Bookkeeping Software for Your Store

Now that you have decided to invest in an ecommerce bookkeeping software for your business, you must keep some things in mind.

Here are some steps to help you select the perfect bookkeeping software for your ecommerce store.

Step 1: Identify features that are most important to meet your business needs.

Step 2: Narrow down the options based on ease of use if that is an important factor for you.

Step 3: Weigh the cost against functionality and choose a software that offers value for money.

Step 4: Check out demos or free trials if available, and compare pricing plans.

Step 5: Consider whether the cost of upgrading the software aligns with your long-term budget.

Step 6: Check if you have direct access to experts to help you make wiser business decisions.

What Is the Best Ecommerce Bookkeeping Software?

With the rise of online shopping and the increasing popularity of ecommerce businesses, there are now many options for bookkeeping software tailored specifically for this market. 

However, amongst these numerous choices, one platform stands out as one of the best solutions available.

We might be playing favorites, but we recommend doola Bookkeeping as the best bookkeeping software for ecommerce entrepreneurs.

It offers a comprehensive range of tools and features designed specifically for ecommerce businesses, such as seamless syncing of sales data and expenses across all platforms.

In addition to integration capabilities, doola’s simple bookkeeping and intuitive dashboard provide real-time reports on revenue, expenses, profits/losses, and other key metrics crucial for making informed business decisions.

Aside from the exceptional software itself, what truly sets doola apart from other bookkeeping services is our team of experienced professionals who offer personalized support to clients.

Whether you need assistance setting up your account or have questions about specific features or reports, our customer service team is readily available to provide solutions promptly.

So, when you have bookkeeping software and a team working in unison to crunch numbers, you never have to worry about misclassifying a transaction or missing a deadline.

Get Started with doola Bookkeeping Today!

Since traditional bookkeeping methods can be time-consuming and not suitable for ecommerce businesses, you should get started with doola Bookkeeping today. 

So, you can say goodbye to manual data entry and spreadsheets and automatically import all your financial data in real time. 

This reduces the chance of human errors and saves you valuable time that can be better spent on growing your business.

Since you already have so much on your plate, we can also help you out during tax season by providing an year-end tax package and generating sales tax returns based on IRS requirements. 

Don’t wait any longer — book a demo today and take the first step towards efficient financial management for your ecommerce store.