5 Best Accounting Software for Ecommerce Businesses in 2025

Efficient financial management is the backbone of successful eCommerce businesses. Accounting software streamlines the process by organizing financial data, simplifying tax preparation, and enabling insightful business analysis. Many businesses even outsource accounting to optimize their workflows further.

With so many options available, finding the right eCommerce accounting software can be overwhelming. To help you decide, we’ve curated a list of the 5 best options for businesses of all sizes—small to large.

Munim

Munim is cloud-based accounting software that offers all accounting, invoicing and taxation solutions in one place. It is a reliable and easy-to-use software for all types of businesses. It features a responsive and secure platform for managing GST billing, invoicing, payments, tax compliance, inventory, accounting, and many more.

With Munim you can get real-time insights into every aspect of your company’s performance and discover new ways to optimize processes. Take control of your business bookkeeping and tax compliance with time-saving automation and remote access. Improve cash flow, get paid faster, and get more done.

No matter how complex is your business, you can manage your bookkeeping effortlessly with Munim anywhere, anytime. And the most interesting part is that Munim is free for the 100 users.

Features

• Maintain your business finances at one place
• Manage your account payables and receivables
• Check your inventory instantly
• Manage invoices automatically
• Manage cash flow confidently
• Analyze incomes and expense
• Add your staff with different user rights
• Invite your CA for collaboration
• Manage multiple businesses with a single login
• Stores payment information with security

Quickbooks

Quickbooks is cloud accounting software for small businesses. Quickbooks is really easy to use. To make eCommerce experience better Quickbooks has integrated with third-party tools. Quickbook has done Shopify integration through an app to make it easy for you to use Quickbooks in your online store.

With Quickbooks, you can manage your business expenses, invoices, cash flow, and many more.

Features

• Cloud accounting
• Invoicing
• Online banking
• Accounting reports
• Cash flow management
• Time tracking
• Accounting reports
• Multiple users
• Free unlimited support

Zoho Books

Zoho books is an all in one cloud-based financial platform for your ecommerce business. From basic accounting to GST compliant everything is done by Zoho Books. Zoho Books is suitable for all types of businesses.

From core accounting, stock tracking, bank reconciliation, and managing projects, to automate workflows, and keep your business GST compliant. Zoho books is easy to integrate with your eCommerce platform and you can automate your bookkeeping and financial workflows.

Features

• Invoicing
• Client Portal
• Bills
• Projects
• Sales orders
• GST
• Audit Trail
• Reporting
• Documents
• Estimates
• Expenses
• Banking
• Inventory
• Purchase Orders
• E-invoicing
• Online payments
• Automation
• Vendor portal

Freshbooks

Freshbooks is an easy to use accounting and bookkeeping software any business size. If your eCommerce business needs an all in one solution the FreshBooks is the right solution for you.

Freshbooks integrates with over 100 great apps to streamline your business, help you connect with your team and clients, and better understand your business.

Features

• Accounting
• Mobile
• Apps
• Payments
• Clients
• Projects
• Estimates
• Proposals
• Expenses
• Reports
• Invoicing
• Time Tracking
• Mileage tracking

Xero

Xero’s online accounting software connects small business owners with their numbers, their bank, and advisors anytime. You can manage everything in one place.

Xero connects with your bank and easily sync bank and financial information. Xero’s features are designed to make life easier for small businesses – anywhere, any time.

Features

• Pay bills
• Claim expenses
• Bank connections
• Accept payments
• Track projects
• Pay runs
• Bank reconciliation
• Manage Xero contacts
• Capture data
• Files
• Reporting
• Inventory
• Send invoices
• Multi-currency
• Purchase orders
• Quotes
• Sales tax
• Analytics
• Accounting dashboard
• Manage fixed assets