The Best Accounting Services for eCommerce in 2025

Key Takeaways for Ecommerce Brands:

1. ‍eCommerce-specific accounting services are essential for online businesses, as they offer specialized capabilities like multi-channel sales integration, real-time inventory tracking, automated reconciliation, and expertise in ecommerce that traditional bookkeeping services lack.
2. The top five alternatives for eCommerce accounting are Finaloop, Pilot, LedgerGuru, Acuity, and eComBalance, with Finaloop standing out for its native eCommerce integrations and real-time COGS tracking capabilities.
3. When selecting an eCommerce accounting service, businesses should prioritize capabilities like automated inventory management, multi-channel sales integration, real-time financial reporting, and a user-friendly interface to effectively manage their online operations.
   

As 2025 seems like it is going to be a tough financial year, with inflation sticky, the market not picking up and tariffs looming, here at Finaloop we wanted to quickly provide some useful information to those we can help: ecommerce businesses.

Of course, this is an industry we know a lot about, and know first-hard how critically ecommerce businesses need ecommerce-specific bookkeeping and accounting solutions to make it in this space.

After all, in the fast-paced world of ecommerce, managing finances effectively can be the difference between thriving and merely surviving. Juggling the intricacies of ecommerce bookkeeping with the help of a generalist, traditional bookkeeping service, can quickly become overwhelming, as traditional tools and services lack essential industry-specific features and capabilities tailored to their needs. As the space is only becoming more and more competitive, this has become indispensable for brand operators and ecommerce-finance professionals alike.

From seamlessly tracking inventory across multiple sales channels to delivering real-time financial insights, eCommerce accounting services help founders address the unique challenges of online businesses. But it goes deeper than that: Ecommerce accounting solutions ensure that entrepreneurs can focus on growth while staying on top of compliance and financial health.

In order to allow businesses in the eCommerce space to choose between the best possible alternatives, we have compiled this article, which sets out the importance and uniqueness of eCommerce bookkeeping and accounting, which features brands should look for, and surveys some of the top eCommerce service providers in the space today, to help you find the perfect fit for your company.

What is eCommerce accounting?

Ecommerce accounting is specialized financial management designed to address the unique challenges and complexities of online businesses.

Unlike traditional accounting that primarily focuses on basic bookkeeping and financial reporting, eCommerce accounting is built to navigate the financial ecosystem of online selling and the challenges it presents.

These challenges include handling multi-channel sales, managing fluctuating and robust inventory, being on top of your cash flow constantly, understanding the seasonality of eCommerce (BFCM sales are obviously different from sales in April) and staying compliant with tax regulations across several jurisdictions. A set of challenges unfamiliar to bookkeepers and accountants who traditionally work with mostly non-ecommerce businesses.

The key distinctions between eCommerce accounting and traditional accounting systems lie in their core functionalities and adaptability to online business models. Traditional systems work well for brick-and-mortar businesses with straightforward revenue streams and predictable financial transactions. On the other hand, ecommerce accounting services are designed to seamlessly integrate with multiple sales channels like Shopify, Amazon, and eBay.

This approach ensures that sales data is automatically synced, reducing the risk of manual entry errors and saving significant time. Additionally, ecommerce accounting services often include capabilities such as real-time inventory updates, precise cost of goods sold (COGS) tracking, and customizable financial reporting, which are critical for online businesses.

By bridging the gap between ecommerce operations and financial management, ecommerce accounting services empower businesses to streamline workflows, gain actionable insights, and focus on scaling their operations without being bogged down by the complexities of bookkeeping. This makes it an invaluable part of the stack for any online business looking to thrive in today’s competitive landscape.

Key Features to Look for in Ecommerce Accounting Services

The best accounting services for ecommerce rely on advanced features that are vital for online businesses but often absent when it comes to traditional bookkeeping that doesn’t focus on eCommerce. These capabilities include:

• Inventory Accounting‍

Integrated inventory management streamlines financial reporting by connecting stock data with accounting records. This integration allows for accurate calculation of the cost of goods sold (COGS), which is essential for understanding profitability.
It means you are getting detailed reports on inventory turnover, helping you identify your best-performing products and optimize your offering accordingly.

Another advantage of advanced inventory management is its ability to handle complex structures. For example, when inventory is composed of recipes, which may be procured from different suppliers. Proper ecommerce inventory accounting knows how to account for the entire recipe and assembly and build landed costs per SKU.

Inventory management is a critical feature of an eCommerce accounting service. It ensures that stock levels are always accurate and up to date. This reduces the risk of overselling or stockouts, which can lead to dissatisfied customers and lost revenue.

• Multi-channel sales integration‍

Ecommerce businesses rarely rely on a single platform for their sales; they often operate across multiple channels such as Shopify, Amazon, Etsy, and eBay. Other channel mixes combine wholesale and retail as well, resulting in what is called an “omnichannel” business.

A proper multi-channel sales integration will allow eCommerce accounting services to sync data from all these platforms into a centralized system. This lets brands view all their transactions, refunds, and fees from various platforms in one dashboard, streamlining financial management.

Integration with multiple sales channels ensures consistent and accurate financial records. For example, it can consolidate sales data across platforms while accounting for different payment gateways and their associated fees. Additionally, multi-channel integration supports inventory updates across platforms.

• Real-time financial reporting 

A powerful feature of ecommerce accounting using cutting-edge ecommerce accounting software is real-time financial reporting, which provides brands instant access to their financial health. Unlike traditional methods that rely on periodic updates and manual reconciliation, real-time reporting ensures that all financial data – sales, expenses, cash flow, etc. – is always up to date. This enables business owners to make informed decisions, whether planning a new marketing campaign, adjusting pricing, or investing in inventory.

The ability to generate detailed and customizable reports is another advantage of real-time financial reporting. Businesses can analyze key performance indicators (KPIs) such as revenue, profit margins, and inventory turnover. These insights help identify trends, such as seasonal spikes in demand, underperforming products, or money-losing promotions, allowing brands to adjust strategies accordingly.
Moreover, real-time cash flow tracking ensures that businesses can address potential liquidity issues before they become critical.

Real-time reporting is particularly valuable in eCommerce, an environment where rapid decision-making can significantly impact success. For instance, businesses can monitor the performance of a flash sale or holiday promotion and adjust quickly to maximize profitability.

• User-friendly interface

A user-friendly interface is a critical feature that ensures accounting software and services are accessible even to those with little or no financial background. With intuitive navigation, clean layouts, and helpful visualizations, user-friendly reports and dashboards make it easy for business owners to manage, read, analyze, and use their finances without feeling overwhelmed by technical jargon or complex processes.

One of the hallmarks of a user-friendly interface is automation, as it minimizes manual inputs by automatically importing sales data, categorizing transactions, and generating reports.

For example, dashboards that display real-time data in a visually appealing format make it easier to understand financial performance at a glance. Step-by-step guides, tooltips, and tutorials further simplify the learning curve, enabling users to become proficient quickly.

User-friendly services and tools don’t just save time; they also reduce errors. By guiding users through tasks, the UX ensures compliance and accuracy. Additionally, mobile-friendly reports allow brand operators to manage their finances on the go, providing convenience and flexibility.

Ultimately, a user-friendly design empowers ecommerce entrepreneurs to take control of their financial management without needing an accounting degree.

The 5 Best Accounting Services for Ecommerce Businesses in 2025

1. Finaloop

Features: 

• An automated, full bookkeeping service with dozens of ex-big-4 eCommerce accountants.

• Native integrations across the eCommerce landscape.

• An eCommerce-dedicated inventory management solution built into accounting software.

• A prebuilt, eCommerce-focused chart of accounts.

• Accounts receivable and accounts payable management.

• Automated transactions categorization.

• Automated reconciliation.

• Tax support.

Pros:

• Seamless integrations with online store platforms like Shopify or Woocommerce and marketplaces like Amazon, Walmart, etc.

• Syncs real-time COGS to your P&L and has top notch inventory capabilities.

• Connects sales channels and payment gateways to pull your data directly from the sources of truth.

• Integrates with your apps, bank accounts, and credit cards for three-way reconciliation – orders to payouts to business bank accounts.

• Accrual versus cash-basis flexibility.

• A team of in-house bookkeepers.

• Customer support 24/7.

Cons:

• Payroll only integrates with Gusto, so other payroll providers pull the data from the bank (and not direct integrations).

• Not ideal for businesses outside the eCommerce space.

2. Pilot

Features: 

• Bookkeeping service.
• Additional add ons such as tax and CFO services (for additional charge).
• Uses third party integrations to automate some of the data collection process.
• Third party (QBO) chart of accounts.

Pros:

• Pricing for starter plans (generally between $349 to $849).
• Offer additional tax services.
• Offer CFO services.
• Syncs sales using third-party (A2X) software.
• Uses inventory/COGs based on user updates.

Cons:

• Horizontal provider working with many industries, impairing its ability to focus specifically on eCommerce.
• Don’t have an eCommerce specific chart of accounts (they generally use QBO)- which means it is not tailored towards eCommerce.
• Financials are not timely, as they are based on third party integrations which generally have delays of several weeks.
• Delays in COGS reporting—Pilot updates inventory in your financial statements every month based on data provided by the customer or from an IMS and updates COGS based on information shared by the customer. This does not allow customers to make real-time decisions relating to COGS or inventory.

3. LedgerGurus

Features:

• Recording transactions, reconciling sales transactions, calculating COGS, and reconciling bank accounts.
• Offers additional services such as sales tax (either DIY, $250 per hour, or they fully handle your compliance with custom pricing- although they do not file or prepare income tax returns), inventory consulting, including integrating IMS tools, payroll support, AP/AR support, clean up of old records and one-time consultation setting up QBO + A2X.
• Use third-party (A2X integration) to pull sales data.

Pros:

• Specialize in eCommerce.
• Have additional add-on services, such as tax and inventory consulting.
• Have access to your sales data through third-party integrations.

Cons:

• Financials are not timely, as they are based on third-party integrations, which generally have delays of several weeks, and they commit to providing financials by the 20th of the month.
• Don’t have a proprietary inventory tool to calculate landed costs.
• Don’t have a chart of accounts specialized for eCommerce.

4. Acuity

Features:

• Acuity’s services range from bookkeeping, controllership, CFO services and tax services.
• Acuity’s bookkeeping services include bookkeeping cleanup, payroll (including outsourcing to one of their partners), expense reporting, invoicing, collections and billpay.
• Use third party (A2X integration) to pull sales data.

Pros:

• Specialize in eCommerce (also provides services to SAAS, crypto and creative).
• Have additional add-on services, such as tax and inventory consulting.
• Have access to your sales data through third-party integrations.

Cons:

• Not cheap (controllership- $142 per hour, CFO- $275 per hour or $4000 per month for weekly insights. Bookkeeping pricing ranges based on each package).
• Financials are not timely, as they are based on third-party integrations, which generally have delays of several weeks.
• Don’t have a proprietary inventory tool to calculate landed costs.
• Don’t have a chart of accounts specialized for eCommerce._‍

5. eComBalance

Features:

• EcomBalance focuses on eCommerce and caters to eCom brands with sales of between $200K and $30M.
• Additional services that they provide are eCommerce (Amazon, Shopify, Ebay, etc.) specific product sales reports, employee payroll reports, AP & AR management, paying invoices and running payroll.
• Use a third party (LinkMyBooks integration) to pull sales data.
• Pricing - monthly fixed price (starting at $509 per month), with additional “catch up” fee.

Pros:

• Specialize in eCommerce.
• Have additional add-on services, like employee payroll reports and AP/AR management.
• Have access to your sales data through third party integrations.

Cons:

• They do not handle inventory or provide an inventory management service, rather, they will make inventory updates in your financial statements every month, quarter, or biyearly as the information is provided to them.
• Do not have proprietary sales integration (they use LinkMyBooks).
• No accrual of expenses on other accounts.
• Not timely- they provide your books by the 15th each month, so you won’t have access to real-time books.

Finding the Best Accounting Services for eCommerce

Choosing the right accounting service is a critical decision for eCommerce brands. With the unique complexities of managing multi-channel sales, fluctuating inventory, and managing cash flow, a one-size-fits-all solution often falls short. By using a service provider tailored to their specific needs, eCommerce businesses can streamline operations, gain accurate financial insights, and stay compliant. And ultimately, save money and grow smarter.

Among the options available, Finaloop stands out as a game-changer. Purpose-built for eCommerce brands, Finaloop's advantage lies in its seamless integrations with all relevant platforms, automated bookkeeping processes, and ecommerce-specific features like real-time reconciliation, and a 6-star service from a team of ecommerce financial experts - backed by cutting-edge technology.

For ecommerce entrepreneurs seeking a seamless and efficient way to manage their finances, Finaloop provides a uniquely tailored approach that prioritizes growth and operational excellence.