QuickBooks Online for Shopify Sellers: Pros, Cons & Alternatives

If you ask any small business owner what accounting software they use, chances are high they’ll say QuickBooks. For decades, QuickBooks has been the default choice for managing business finances, and for good reason. It’s powerful, comprehensive, and trusted by millions of entrepreneurs and accountants worldwide. As a Shopify seller, it’s natural to consider it as the foundation for your financial tech stack.

But running a Shopify store isn’t like running a traditional brick-and-mortar business. The world of e-commerce has its own unique financial challenges, from tracking payment processor fees to managing inventory costs across thousands of transactions. This raises an important question: is the world’s most popular accounting software the right choice for the specific needs of a modern online brand?

This guide provides an honest review of using QuickBooks Online (QBO) for your Shopify store. We’ll cover its key features, weigh the pros and cons, discuss pricing, and explore powerful alternatives to help you decide if it’s the best financial tool to build your business on.

What Is QuickBooks Online?

QuickBooks Online (QBO) is a cloud-based accounting software created by Intuit. It allows business owners to manage their income and expenses, track financial health, and streamline their bookkeeping. From sending invoices and paying bills to running financial reports and preparing for tax season, QBO aims to be the central hub for a company’s finances.

Unlike its original desktop version, QBO is accessible from any device with an internet connection, making it a flexible solution for on-the-go entrepreneurs. Its massive market share means it has a vast ecosystem of integrations, connecting with thousands of third-party apps, banks, and payment processors. For Shopify sellers, this means you can connect QBO to your store, but as we’ll see, how you make that connection matters.

Key Features of QuickBooks Online for Shopify Sellers

While QBO is a generalist tool, it has a robust set of features that can be configured to serve a Shopify business.

Comprehensive Accounting and Bookkeeping

At its core, QBO is a full-featured double-entry accounting system. This means it can handle all the fundamental tasks required for clean, audit-proof books. You can create a customized Chart of Accounts, run standard financial reports like the Profit & Loss (P&L) and Balance Sheet, and track all your business expenses. This solid foundation is essential for any serious business.

Integrations with Shopify and Other Tools

QBO integrates with a vast array of business software, including Shopify. However, the native Shopify integration is often too simplistic for growing stores, as it can clutter your books by syncing every single order. Most seasoned sellers use a third-party connector app (like A2X, Link My Books, or Synder) to bridge the gap. These apps summarize daily sales, fees, and taxes into neat journal entries, giving you accurate data without overwhelming your QuickBooks account.

Reporting and Analytics

QBO offers a wide range of customizable reports that provide deep insights into your business’s financial performance. You can track sales trends, monitor expenses by category, and create budgets to plan for the future. While it doesn’t offer e-commerce-specific metrics like Customer Lifetime Value out of the box, its powerful reporting engine allows you or your accountant to analyze the financial health of your business from multiple angles.

Pros and Cons of QuickBooks Online

Using the industry-standard software comes with significant benefits, but it also has its drawbacks, especially for e-commerce.

Pros

• Universally Recognized: Nearly every accountant, bookkeeper, and tax professional in North America knows how to use QBO. This makes collaboration with financial experts seamless.
• Incredible Flexibility: QBO is designed to serve every type of business, from freelancers to construction companies. This flexibility means it can handle complex scenarios, like a business that has both an online store and a physical retail location.
• Massive App Ecosystem: With thousands of integrations, you can connect QBO to almost any tool you use, from payroll services to CRM software, creating a unified back-office system.
• Scalability: QuickBooks offers different tiers, including an “Advanced” plan that can support larger, more complex businesses as they grow.

Cons

• Not E-commerce Native: QBO was not built with e-commerce in mind. It struggles with concepts like payment processor reconciliation and accurate Cost of Goods Sold (COGS) for high-volume stores without significant manual work or extra apps.
• Requires Third-Party Connectors: To use QBO effectively for Shopify, you almost always need to pay for an additional connector app, adding to your monthly costs and complexity.
• Steep Learning Curve: Because it’s so comprehensive, QBO can be overwhelming for beginners. Setting it up correctly for e-commerce requires accounting knowledge to avoid common pitfalls.

Pricing: How Much Does QuickBooks Online Cost?

QBO’s pricing is based on a tiered subscription model, with plans generally ranging from $30 to over $200 per month. The plan you need depends on the features you require, such as inventory management, project tracking, or advanced analytics.

However, the subscription fee is only part of the total cost for a Shopify seller. You must also factor in the cost of a connector app, which can range from an additional $20 to $100+ per month depending on your order volume. Therefore, the true monthly cost of running QBO for a Shopify store is often between $50 and $300, before factoring in any bookkeeping or accounting fees.

Alternatives to QuickBooks Online for Shopify Sellers

If the limitations of QBO for e-commerce have you concerned, you’re in luck. A new wave of financial tools has emerged that are built specifically for online brands.

The most notable alternative is Finaloop. Finaloop is an automated accounting and bookkeeping service designed from the ground up for DTC businesses. It integrates directly with Shopify, Amazon, Stripe, and PayPal in real-time, automatically reconciling transactions and providing an accurate, live view of your profitability.

Here’s how Finaloop differs from QBO:

• It’s All-Inclusive: Finaloop replaces your QBO subscription, your connector app, and often your human bookkeeper with a single service.
• It’s E-commerce Native: It automatically calculates COGS, understands payment processor fees, and presents data in a way that makes sense to online sellers.
• It’s Automated: It’s designed to be a “hands-off” solution, giving you tax-ready books without the manual data entry.

While QBO is a blank canvas that requires an artist (your accountant) to paint a picture, Finaloop is more like a high-resolution photograph—it captures reality automatically and accurately.

Is QuickBooks Online Right for Your Shopify Store?

The decision to use QuickBooks Online depends on your business model and your comfort level with accounting.

QuickBooks Online is the right choice if:

• You work with a traditional accountant or CPA who requires you to use it.
• Your business has complex needs beyond e-commerce, such as wholesale, physical retail, or service-based revenue streams.
• You have an in-house bookkeeper or are willing to learn the intricacies of accounting to set it up correctly.

However, if you are a pure-play e-commerce brand looking for an automated, accurate, and hands-off solution that gives you real-time insight into your profitability, an alternative like Finaloop may be a more direct path to financial clarity.

For many Shopify sellers, QBO remains a reliable, if imperfect, choice. It’s a powerful foundation, but be prepared to build on it with the right apps and expertise to make it truly work for your online business.

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