Top Accounting Software for Small eCommerce Businesses in 2024 

Picture of Gary Jain
Gary Jain

Founder, Ledger Labs

ecommerce accounting software 

Table of Contents

If you have a business, you need an accounting software. With online sales soaring and competition scarier than ever, the right accounting software can either make or break your business. 

Think about it. You are already overseeing the sales made from your website. Apart from that, you also have to look at the sales made on eBay or Amazon. If that is not enough on your plate already, you also have to juggle inventory, taxes, and understand whether or not you are making sufficient profits. Truth be told, all of this can be pretty time-consuming and difficult to control when done together.

This is exactly the solution Ecommerce accounting software offers for your small business. In fact, Ecommerce sales are forecasted to hit a solid $6.3 trillion globally. Looking far ahead, this number does look promising. Regardless, that’s still a lot of transactions to keep track of.

In this blog post, we will give you a sneak peek into some of the best accounting eCommerce software. In fact, we have already done the heavy lifting – figuring out the features, pros, and cons. Altogether, they will definitely give you an idea of what to choose from the lot. 

So, let’s cut through the jargon and dive right in.

Understanding the Needs of Small Ecommerce Businesses

There are several needs a small Ecommerce business has. To be precise, they need accounting software, which:

  1. Track sales across multiple platforms: Your business probably sells through several channels, such as your website, eBay, Amazon, Etsy, and many others. To make it seamless, the software should consolidate sales data from all the given sources. This is to offer a detailed, comprehensive view of the revenue you are generating.
  2. Handles inventory in real-time: There is absolutely no doubt that you need to keep a good eye on your inventory levels to prevent stockouts or overstocking. This is especially a major need for small businesses because it helps them understand what’s in stock, what’s selling extremely fast, and the ones that require rearrangement or reordering.
  3. Ensure complete tax compliance: As you know already, different areas or regions have different tax laws. That being said, most eCommerce businesses usually deal with more than one tax jurisdiction as well. When you have the right accounting software, it helps you stay compliant by organizing your records properly and evaluating your taxes accurately.
  4. Supports multi-currency transactions: More and more businesses are selling their goods and services internationally. In 2023, global eCommerce sales touched $5.82 trillion. In a way, this goes to show that when you sell online, you will have a massive opportunity. But, if you sell globally, the software you use must handle multi-currency transactions without a hitch.

Ecommerce Accounting Software Key Features to Look for in 2024

When you are choosing an Ecommerce accounting software for small businesses, all you need to think about is how to make your operations more streamlined and manage your finances efficiently.

Here are some key features you must look for:

Multi-Channel Sales Integration

The software you are going to choose should seamlessly integrate with popular eCommerce platforms, such as Shopify, Amazon, or eBay – among others. This step helps sync multitudes of sales data automatically. Thus, it reduces your workload and saves you from making mistakes.

Real-Time Inventory Management

Make sure you look for real-time inventory management in order to tackle stock levels, oversee reorders, and avoid stockouts or overstocking. When you have automated notifications for low stock levels, it helps you stay posted about your needs.

Automated Bookkeeping

The software you choose must automate expense tracking with credit cards and bank accounts. This means it should largely categorize the transactions automatically. Plus, certain features, such as payment reminders, automated invoicing, and payment gateway integration, just manage to streamline billing processes twofold.

Tax Compliance

You need to make sure the software can automatically estimate sales tax for specific jurisdictions. In fact, it should also be able to prepare tax reports in full compliance with the laws and regulations.

Customization and Flexibility

There’s no doubt that, with time, your business will expand more and more. With your growing needs and changing necessities, the software should evolve too. That being said, look for accounting software that offers advanced features as required. Plus, make sure the software has enough customization to fit your needs as a small business owner.

If you need more help understanding the features in depth, you can get help from an expert accountant for eCommerce business.

Looking to know more about the features you would need for your business?

Top Accounting Software for Small Ecommerce Businesses in 2024 

Some of the top names in the market are:


Known for its easy-to-use interface, Xero is a cloud-based accounting software. It is an extraordinary tool for eCommerce small businesses. 

Plus, this accounting for eCommerce business software is also widely renowned for its scalability and its integration with several third-party applications. It is pretty ideal for growing businesses that require real-time financial insights.

Some of its key features include:

  1. Real-time financial reporting
  2. Feeds from any number of bank accounts
  3. Multi-currency support
  4. Easy payroll management
  5. Management of fixed assets
  6. Manage and calculate sales tax
  7. Integration with more than 800 apps

Pros of Xero

  1. Scalable with business growth
  2. Get access anytime, anywhere
  3. Intuitive and clear dashboard
  4. Supports unlimited users

Cons of Xero

  1. Many find it tedious to learn the application in detail
  2. It comes with limited capabilities for larger enterprises
  3. Some users find the mobile app limited
  4. May not be suitable for complex inventory needs in lower plans

QuickBooks Online

Quickbooks Online is an amazing Ecommerce accounting software, all in all. It is a widely used accounting software that is meant for small businesses. 

Not to mention, it also comes with a comprehensive suite of features. Some of the well-known ones are managing finances, tracking sales, and guaranteeing overall compliance.

Some of its key features include:

  1. Multi-channel sales tracking
  2. Bookkeeping automation and mileage tracking
  3. Automatically syncs sales data from all channels
  4. Real-time tracking of inventory levels
  5. Consistent alerts about low stock levels or overstocking
  6. Sales tax calculations for several tax jurisdictions
  7. Automated and detailed payment reminders 

Pros of QuickBooks

  1. Easy-to-navigate and simple UI 
  2. Consolidated and robust mobile app access
  3. Well integrates with third-party apps for better operations
  4. Offers a range of accounting tools, from payroll integration to invoicing

Cons of QuickBooks

  1. QuickBooks Online can be expensive as opposed to other accounting software
  2. Suffers occasional performance issues, such as slowdowns dealing with large data volumes
  3. The features are too extensive to get accustomed to in a short period of time

Epicor Management

Epicor Management is an awesome accounting software for small businesses. It is a fully integrated enterprise resource planning solution (ERP) that caters to several business needs. 

In fact, some of them include inventory control, accounting, sales, production, and human capital management. You get quite a lot of things under one roof. It also simplifies both accounts payable and accounts receivable processes as well. If you are looking for a solution that scales gradually with your business, this may be the answer you need.

Some of its key features include:

  1. Offers a comprehensive, in-depth, and unified view of your finances
  2. Shows a complete, 360-degree view of customer interactions
  3. Comes with tools for CRM, supply chain management, and project management
  4. Comes with modules for manufacturing, distribution, retail, and services

Pros of Epicor Management

  1. Comes with plenty of user interface options, like Classic and Modern
  2. Versatile deployment along with the capability to add modules when required
  3. Streamlined integration with existing systems through advanced EDI software
  4. Customization flexibility and features that automatically updates other screens

Cons of Epicor Management

  1. Not very user-friendly with clocking in and out of jobs being tedious
  2. Past issues reported about lagging performance and buggy releases
  3. Interface, often, too basic – with some page navigations too difficult
  4. Inbuilt report compatibility with Excel might not be as optimal
  5. Customer support can be inconsistent at times during peak hours

ODOO Management

Known best for its fully integrated, open-source business applications, Odoo is one of the best tools on the market that has an in-depth accounting module. 

In fact, it is well known for its ability to meet almost all the needs of small to medium-sized businesses. As you can guess, it is one of the most amazing tools out there for Ecommerce operations as well. Plus, its versatility makes it all the more famous.

Some of its key features include:

  1. Plenty of integrated apps for Customer Relationship Management (CRM), project management, inventory, and more
  2. In-depth P&L statements, balance sheets, and cash flow reports
  3. Real-time currency conversion and multi-currency support
  4. Automated transaction import and reconciliation
  5. Meticulous inventory tracking and management
  6. Integration with sales and purchase modules
  7. Generation of professional invoices automatically

Pros of Odoo Management

  1. A suite of applications that include all factors of business management
  2. Heavily customizable and secure, allowing seamless fit of your needs
  3. Just like most, it is easy to navigate and incredibly intuitive
  4. Highly suitable for businesses wanting to scale up
  5. Cost-effective and has the versatility of open-source software

Cons of Odoo Management

  1. Extensive features can be confusing to those with little needs
  2. The initial setup can be too tedious for first-time users
  3. Some advanced features are available for enterprise solutions only
  4. While very user-friendly, the features can be confusing to get familiar with

NetSuite Management 

NetSuite cloud accounting software allows you to record transactions, tackle accounts payables and receivables, close the books, and also collect taxes. It is one of the most well-known, preferred, and interactive Ecommerce accounting software for businesses. 

In fact, it provides real-time access to your financial information. What’s more, it offers you greater and more firm control over your financial assets.

Some of its key features include:

  1. Comprehensive accounting, including general ledger (GL), Accounts payable / receivable, fixed assets, etc
  2. Real-time reporting with customizable dashboards and KPIs
  3. Automated financial consolidation and bank reconciliation
  4. Seamless inventory tracking across several locations
  5. Streamlined and immaculate order-to-cash process
  6. Easy CRM integration and improved sales performance

Pros of NetSuite Management

  1. Real-time sync of sales, inventory, and customer data
  2. Guarantees security of business operations
  3. Gradually grows with your business without a hitch
  4. Seamlessly covers all aspects of business management
  5. Customizable and tailored dashboards for every need
  6. Streamlined collaboration across departments with centralized data

Cons of NetSuite Management

  1. More expensive than most of the other accounting software
  2. The setup and implementation are too laborious and difficult
  3. The amount of customization present can be too hard to learn over time
  4. Customer support can be inconsistent, particularly for initial setup

Acumatica Management 

This is a software that is quite the talk of the town. Acumatica is a cloud-based ERP (Enterprise Resource Planning) solution that supports and caters to small to medium-sized businesses. 

This is quite a fantastic software for small ecommerce businesses. With this software, you can do a lot of things. Starting from financial management to inventory and CRM, it offers a suite of features you’d like to get your hands on.

Some of its key features include:

  1. Real-time financial reporting and dashboard customization
  2. Seamless inventory management and streamlined tracking
  3. Support for multiple currencies over different locations
  4. Streamlined tracking of project revenues and costs
  5. Consistent support for multi-channel retailing

Pros of Acumatica Management

  1. Real-time visibility into field operations, such as labor costs
  2. Efficient and streamlined management of subcontractors
  3. Track and manage inventory levels, progress tracking, payments, etc
  4. Better collaboration between different departments
  5. Guarantees protection of sensitive data
  6. Enhanced role-based dashboards and configurable workflows
  7. Generate reports and gain insights into the business’s well-being

Cons of Acumatica Management

  1. Comes with a high initial set-up cost and ongoing subscription fees
  2. Difficult to learn during the initial days due to hard-to-grasp concepts
  3. Requires substantial time and resources for its customization
  4. Difficulty integrating a handful of third-party applications

Sage Intacct Management 

Sage Intacct Management is a software that a lot of people like. The reason is its neat, tidy, and interactive dashboard. 

But, that’s not just it. 

People like this ecommerce accounting software for small businesses because of its strong accounting and incredible financial abilities. It is well-suited for small to medium-sized enterprises (SMEs) that need heavy financial management.

Some of its key features include:

  1. Fully cloud-based and can be accessed from anywhere, anytime
  2. Quite an extensive marketplace for add-ons and functionalities
  3. Regular and automatic updates for security enhancements
  4. Multi-dimensional reporting and advanced capabilities
  5. Supports financial consolidation across multiple departments

Pros of Sage Intacct Management

  1. Preferred by the American Institute of CPAs (AICPA)
  2. Fully compliant with Health Insurance Portability and Accountability Act (HIPAA) regulations
  3. Makes room for team collaboration and productivity
  4. Provides a firm scalability solution for small businesses
  5. Guarantees security, safety, and overall protection of sensitive data

Cons of Sage Intacct Management

  1. Same-day transactions cannot be downloaded until the following date
  2. Difficulty adding Purchase Order (PO) number to an old invoice from a locked period
  3. Some reports are not as simply identifiable and decipherable
  4. Some of the many functionalities and features are cumbersome to execute

Microsoft Dynamics Management

Again, this is an amazing tool for your small ecommerce business. Microsoft Dynamics 365 is a cloud-based, powerful suite that combines ERP and CRM. It makes business growth a breeze with its capabilities. In fact, its robust customer engagement and streamlined operations make it even better.

Some of its key features include:

  1. Offers modules for sales, operations, finance, customer service, and more
  2. Real-time financial reporting that has customizable dashboards
  3. Efficient and hassle-free integration of procurement and logistics
  4. Efficient CRM integration and great service operations
  5. Advanced tools for error-free project costing and analysis

Pros of Microsoft Dynamics

  1. Powerful integration with other Microsoft products, like Office 365
  2. Dynamics 365 helps centralize business apps into one integrated platform
  3. Dynamics 365 was built on Azure, a cloud environment supporting several security features
  4. Powerful decision-making with advanced analytics
  5. Seamless and strong support for operations held globally

Cons of Microsoft Dynamics

  1. Software can be expensive as you need to pay for hardware, cloud storage, etc
  2. Microsoft can be inconsistent when offering documentation around migrating data
  3. The software can come with a good chunk of performance issues over time

How to Choose the Right Software for Your Small Ecommerce Business?

Before you choose accounting software for your small eCommerce business, you need to weigh your pros and cons. That also means it does not matter what plan or feature you like – if it is not serving the right purpose, it is not a wise decision after all. Here are some key factors you need to understand:

1. Assessment of your needs

Understand the size and complexity of your business. That’s the first step. Are you a solopreneur or an individual with a team? How complicated is your inventory and overall product?

2. Feature consideration

Next up, look at all the features you need. It can be a product listing, order processing, or something more complex in nature. Weigh in if you need advanced features or lower packaged features does the job well already. Only after you have understood these needs can you now look for budgetary boundaries.

3. Software Evaluation

Now that you know your requirements, consider the scalability of the platform, the integrations that you would need, and the type of customer support reputation of the software.

4. Free trials

Most of the platforms offer free trials. You can easily take a test drive and see for yourself how the software is coming out. That way, it becomes easy to take the next step with a confirmation ahead of time.

In all cases, just remember that the budget you have is not everything. You need to weigh all your needs against your goals.

Expert Tips for Implementing Accounting Software 

Before implementation, remember these key tips:

  1. Have a mind map of your business requirements and goals before choosing the software.
  2. Make sure to research the market, read several reviews, and compare features.
  3. Due to its confusing nature, provide proper training for your team members to ease the process.
  4. Make sure to plan and validate data migration to prevent mishaps.
  5. At times, it is best to conduct pilot testing to pinpoint and fix underlying problems.

Future Trends to Look for in Ecommerce Accounting Software

Artificial Intelligence (AI) and machine learning (ML) are really turning the page for future trends in eCommerce accounting software. These will be technological breakthroughs that allow businesses to decipher and adapt to data that comes to knowledge at odd times. 

This means that the market is already changing pretty fast, and soon enough, AI and ML will make procedures far simpler. How? It can forecast changes accurately and on time. Nonetheless, the future of eCommerce accounting software does look bright.

Bottom Line

There you have it. A detailed look at everything you need to know before making a choice as big as choosing the right software. Nonetheless, before making the choice, look at your needs. 

You may scale in three years down the road, but choosing a package that caters to that time may be wrong now. What you need right now is a plan and a whole package that caters to your current needs, not your future ones. So, to say the least, make a choice that suits your business size, model, strength, and requirements.

If you have more questions, drop a line or book a consultation with experts at The Ledger Labs who have more than 12 years of experience. Our specialists are here to help you make the right choice, regardless of any external factor whatsoever. Get in touch today.

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