The success of your online business hinges more on your accurate accounting and streamlined financial management than you might care to acknowledge—which makes your accounting software one of the most impactful implementations in your tech stack. You need a solution that addresses every element of accounting, including budgeting, reporting, 1099 filing, bookkeeping, and revenue tracking.
Ensuring your online accounting software helps monitor tax compliance, tax calculations, and multi-channel sales is crucial for eCommerce businesses. For example, you’ll need to watch your sales in certain states as they approach the economic nexus that initiates your tax obligation. Some states determine this by dollar amount and others by total transactions.
But broadly, these considerations should come before any other factors:
- Ease of use: Pick user-friendly cloud-based eCommerce accounting software to ensure seamless transition and adoption. Full-featured and complex solutions may be appealing, but if you can’t effectively use one of the most important tech platforms in your stack, it only leads to frustrations and (costly) mistakes.
- Scalability: The software must adapt to your business growth and needs. As your business grows, it should handle a surge in users, transactions, and workflows.
- Integrations: Regardless of your eCommerce platform, the software must ensure compatibility to ensure a ‘single source of truth’ for data across all systems and eliminate the need for manual data entry. Your accounting software should integrate with bank accounts, accounts receivable, and payment processors, but other systems may be more difficult or require custom connectors.
- Automation: One of the most valuable reasons to implement accounting software is to automate tasks like payment reminders, sales data entry, and tax deductions. This prevents human errors caused by manual entries and immensely speeds up processes.
- Reporting and analytics: The right software must offer detailed financial reports and insightful analytics to simplify the reconciliation of audits and records. Your accountant should have access to reports with just a few clicks.
- Support: Ensure the vendor offers professional support via email, call, chat, and ticket system. They should be available whenever you need help with integrations, security, compliance, and implementation.
When searching for the right software, consider your business needs and processes, such as the volume of transactions, inventory management, multi-currency support, and the required automation. Looking at user reviews on sites like G2 and Capterra will also provide you with some insight into the actual user experiences.
Top eCommerce Accounting Software for 2025
Here are some of the top cloud-based accounting software solutions to consider when considering software for your eCommerce business:
| Software Name | Pricing | Ease of Use | Top Features | Integrations | Scalability | Best For |
| QuickBooks Commerce | Starts at $39/month | Medium | Multi-channel inventory, automated reporting, expense tracking | Shopify, Amazon, eBay, WooCommerce | High | Small and Medium eCommerce Businesses |
| Xero | Starts at $12/month | High | Bank reconciliation, invoicing, project tracking, custom pricing | Shopify, Stripe, PayPal, Square | Medium | Freelancers and Small Teams |
| FreshBooks | Starts at $15/month | High | Expense tracking, time management tools, invoicing | Stripe, PayPal, Shopify | Low | Solopreneurs |
| Zoho Books | Starts at $10/month | High | Client portal, project management, automated workflows | Stripe, Shopify, PayPal | Medium | Budget-Conscious Small Businesses |
| A2X | Starts at $19/month | Medium | eCommerce-specific accounting, transaction matching | Shopify, Amazon | Medium | Amazon and Shopify Sellers |
| Sage Intacct | Custom Pricing | Medium | Custom reporting, compliance support, real-time visibility | Salesforce, PayPal, Shopify | Very High | High-Growth Startups |
Generally, your ideal accounting tools depend on your budget and business size.
For instance, QuickBooks Commerce suits small and medium businesses with large transaction volumes that want a reliable accounting solution. FreshBooks, Zoho Books, and Quickbooks Online work well for small business owners and budget-conscious eCommerce startups.
Regardless, the software you select may not be capable of all the integrations, automation, reporting, and other backend capabilities you’re looking for—at least not without some professional help.
Analysis of the Top Accounting Software Picks
Below, we share some of our favorite picks from the chart to provide suggestions for specific use cases and businesses.
QuickBooks Commerce: Best for Small and Medium Businesses
With QuickBooks Commerce, you get an all-in-one solution for tracking costs, taking payments, and optimizing sales channels. It consolidates all your orders and payouts in one central place for effortless management, and its monthly subscriptions range from $35 to $235.
QuickBooks Online integrates with Amazon, eBay, Etsy, and Shopify, allowing you to see income and expenses in one place. It separates your revenue from fees and taxes, mapping it to the right accounts and simplifying the preparation of business activity statements (BAS).
Zoho Books: Best Budget-Friendly Solution
Suppose you’re looking for a budget-friendly solution. In that case, Zoho Books is a powerful solution offering a free accounting software plan for businesses with a turnover of less than $50k annually. Paid plans range from $10 to $60 monthly per organization, billed annually.
Zoho Books supports core features like banking, quotes, expenses, bills, sales orders, reporting, and purchase orders. With a paid plan, you get customizable templates and the ability to manage recurring costs. Zoho allows you to automate regular accounting tasks for ample efficiency.
FreshBooks: Best for Solopreneurs
FreshBooks is the go-to accounting software for solopreneurs, costing between $9.50 and $30 per month. It enables you to track income, expenses, assets, and loans, and you can create insightful reports to see where your business stands.
The software supports double-entry accounting to keep eCommerce business owners organized for tax time, make data-driven decisions, and stay compliant. Its customizable Chart of Accounts lets you track every number as your business grows, and you can use automated bank reconciliation to reconcile your books quickly.
A2X: By eCommerce, for eCommerce
If you’re seeking an accounting solution specifically developed for eCommerce by long-time industry veterans who’ve packed orders to ship themselves, A2X may provide your platform. The transaction matching capabilities, in particular, will help omnichannel sellers reconcile their books.
With Amazon, Shopify, eBay, Etsy, Walmart, and multi-channel integrations available, A2X can centralize your accounting processes. Alternatively, you can leverage A2X to transform and reconcile your data pulled from eCommerce platforms before importing it into QuickBooks, Xero, or NetSuite.
Disclaimer: Nimbl holds an official partnership with A2X.
Nimbl Accounting Solutions: Your Trusted Accounting Partner
Although not so much software, Nimbl offers a full-service accounting team to guide you through your software selection and implementation process. The team assesses your financials with the expertise expected from CFOs, controllers, and finance directors, providing strategic financial guidance and best practices for enhancing your eCommerce accounting foundation.
Like the software-as-a-service (SaaS) accounting solution you’re looking to implement, Nimbl offers “Accounting as a Service” (AaaS). We outfit your eCommerce business with tailored accounting solutions and accounting specialists who help align everything from basic bookkeeping and your accounting software’s cybersecurity to acquisitions and exit planning.
Decision Guide: Which Accounting Software Is Right for Your eCommerce Business?
Which software solution is ideal for your eCommerce business? Here are factors to consider when making the decision:
- Business size: Small and high-growth companies have different needs, which impact their software choices. For instance, a business might need a cloud-based accounting solution that scales with its operations or supports extensive customization.
- Sales volume and complexity: High sales volumes and complex accounting processes require advanced software. You need a solution that adapts to increasing storage and processing needs without complexities.
- Integrations: Review your tech stack and pick a solution compatible with existing tools to ensure integrations and automation function seamlessly. Integrations should include major eCommerce platforms like Shopify, WooCommerce, or BigCommerce.
- Support: The vendor must offer support to help resolve issues whenever you encounter them. Ensure they have multiple support channels, including calls, chats, emails, and forums.
- Budget: Accounting software has custom pricing or monthly subscriptions. Evaluate the different pricing models and understand your business needs to pick a solution that fits your budget.
- Security: Inspect the software to ensure it supports different security features and frameworks, such as encryption, compliance, data security, and firewalls. The vendor must provide regular updates to address bugs and vulnerabilities.
Do you need help determining which software best fits your needs? Contact Nimbl for a free consultation to discuss your needs and get tailored recommendations. We assess your business’s financial health and provide proven solutions that support business growth and enhance your accounting process.
Nimbl: Beyond Cloud Accounting for eCommerce
Cloud accounting platforms will help maintain books, monitor tax compliance, streamline inventory management, automate transactions, track payments, and reconcile bank accounts, providing visibility into your financial data and health. Picking which accounting software for eCommerce suits your operations best comes down to usability, business size, budget, integrations, cost, and customization.
But what comes next?
You might find your cloud accounting software a bit limited if you’re also looking to optimize the rest of your tech stack, develop custom reports, identify savings and reinvestment opportunities, or start planning long-term business goals with the help of a fractional CFO, controller, or finance director.That requires a strategic finance partner as your guide. Let’s talk if you’re looking for one that stays Nimbl to meet your needs.
