Your payment processor isn’t just a tool, it’s the backbone of your cash flow. For businesses using QuickBooks, QuickBooks Payments may seem like the obvious choice, but what about Stripe, Square, or PayPal?
Each platform has strengths, but they’re built for different business needs. Some work better for e-commerce, while others are optimized for retail or service-based businesses. While they all can integrate with QuickBooks, the ease and effectiveness of those integrations vary.
In this article, we’ll break down the differences between QuickBooks Payments, Stripe, Square, and PayPal, comparing fees, ease of use, and best use cases so you can make the smartest decision for your business
Comparing QuickBooks Payments, Stripe, Square, and PayPal
We’ve worked with countless clients who chose a processor based on convenience, only to realize later that high fees, poor integration, or complicated bookkeeping were costing them time and money.
Here’s what we’ve learned: the best payment processor depends on how your business operates. Some are built for e-commerce, others for retail, and some work best when integrated directly into your accounting system.
Let’s break it down:
- QuickBooks Payments – If you’re already using QuickBooks for accounting and invoicing, this is hands-down the easiest and most efficient option. It syncs seamlessly with your books, so transactions, invoices, and payments are automatically recorded with no third-party apps and no extra work.
- Stripe – If you run an e-commerce business or need advanced online payment features, Stripe is a powerful tool. It offers deep customization, but it’s more complex to set up and doesn’t integrate natively with QuickBooks (meaning you’ll need an extra tool to keep your books straight).
- Square – If you’re in retail, food service, or any brick-and-mortar business, Square’s POS system is one of the best. It makes in-person transactions simple, but getting that data into QuickBooks can take some extra steps.
- PayPal – If you do a lot of international sales or online transactions, PayPal is a familiar and trusted option. But we’ve seen clients struggle with its bookkeeping. Since PayPal holds funds separately, it can complicate cash flow tracking in QuickBooks.
We’ve helped businesses untangle payment processing headaches more times than we can count. In almost every case, if you’re already using QuickBooks, QuickBooks Payments is the most seamless choice. In the next section, we’ll walk through the costs so you can decide if it’s the right move for your business.
Understanding Fees: What Will It Cost You?
Payment processing fees can eat into your profits fast, and we’ve seen plenty of businesses get caught off guard by hidden costs. While every provider charges transaction fees, the differences in pricing structures can make a big impact on your bottom line, especially if you process a high volume of payments.
Here’s how Stripe, Square, PayPal, and QuickBooks Payments compare:
Stripe: Charges a flat 2.9% + 30¢ per transaction for online credit card payments, with additional fees for international cards and currency conversion.
Square: 3.5% + 15¢ for manually entered cards, but 2.6% + 10¢ for swiped/tapped transactions. Square offers hardware bundles for in-person sales but charges additional fees for advanced POS features.
PayPal: Charges 3.49% + 49¢ per transaction for online credit/debit card payments. There are additional cross-border fees for international payments, and PayPal also takes a cut of refunds, meaning you don’t get processing fees back if you issue a refund to a customer.
QuickBooks Payments: No monthly fee if you’re using QuickBooks Online. Transaction rates vary:
- 2.99% for card transactions (swiped, dipped, or tapped).
- 3.99% for keyed-in transactions.
- 1% (max $10 fee) for ACH bank transfers (a cost-saving option for larger payments).
- Instant deposits are available for an extra 1.75% fee.
QuickBooks Payments Pricing Varies by Product
Unlike other payment processors, QuickBooks Payments pricing depends on which QuickBooks product you’re using. For example, QuickBooks Desktop versions require a monthly fee, but they offer lower per-transaction costs in some cases.
If you’re interested in learning more about how QuickBooks Payments pricing compares across different QuickBooks products, we’ve written an entire article on the topic!
Read More: Everything You Need to Know About Using Quickbooks Payments
What This Means for Your Business
If you’re already using QuickBooks, sticking with QuickBooks Payments eliminates the hassle of third-party integration and gives you lower ACH rates, a huge advantage for businesses that process large invoices. However, if your business is mostly online, Stripe might offer better flexibility, and Square is ideal for in-person sales.
At the end of the day, choosing the right processor isn’t just about rates, it’s about how seamlessly your payments sync with your books. If there’s one thing we know from working with businesses over the years, it’s that manual data entry and disconnected systems lead to wasted time and costly mistakes.
Related Reading: How to Bill and Get Paid Recurring Payments in QuickBooks
Which Payment Processor Is the Easiest to Set Up and Manage?
We’ve seen too many businesses struggle with payment systems that require extra steps, don’t sync properly with accounting software, or leave them manually chasing down transactions. So, how do QuickBooks Payments, Stripe, Square, and PayPal compare when it comes to ease of use and setup?
QuickBooks Payments: Built for QuickBooks Users
If your business already runs on QuickBooks Online, Advanced, or Enterprise, setting up QuickBooks Payments is a no-brainer. It’s already integrated, meaning you can start accepting credit cards, ACH payments, and even Apple Pay directly through invoices, sales receipts, or online payment links, without using third-party connectors.
Setup is as easy as activating Payments in QuickBooks, linking your bank account, and customizing your payment settings. Transactions automatically sync with your books, eliminating the need for manual entry.
Beyond just credit cards, QuickBooks Payments also streamlines ACH bank transfers, mobile payments, and even recurring billing, so your entire payment process is built into the same system where you track expenses and revenue.
Related Reading: Which QuickBooks Version Is Right For Me? [2025]
Stripe: Highly Customizable, But Requires More Work
Stripe is designed for developers and businesses with unique payment needs, especially in e-commerce. While powerful, it’s not plug-and-play, you’ll likely need some technical expertise or third-party apps to integrate it properly with QuickBooks.
If your business relies on advanced checkout flows, subscription billing, or international payments, Stripe is a strong option, but the tradeoff is a more complex setup.
Square: Best for In-Person Sales, But Extra Steps for Accounting
Square is a great choice for brick-and-mortar businesses with a focus on in-person sales. It offers user-friendly POS hardware and mobile payment options, making it simple to accept payments in-store or on the go.
However, it doesn’t sync natively with QuickBooks, meaning you’ll need to connect it via Square’s integration tool or a third-party app. This adds an extra layer of work when reconciling transactions.
PayPal: Familiar, But Can Complicate Bookkeeping
PayPal is widely used for online and international transactions, but it doesn’t deposit payments directly into your bank account like other processors, it holds funds in your PayPal account until you manually transfer them.
This can create a major bookkeeping headache, as PayPal transactions need to be manually categorized in QuickBooks, and fees aren’t automatically deducted in the same way other processors handle them.
Related Reading: 5 QuickBooks Features to Maximize Your Profits
Which One is Right for You?
- If you already use QuickBooks, QuickBooks Payments is by far the easiest option, you can accept credit cards, ACH payments, and even mobile payments without extra integrations.
- If your business is heavily e-commerce-based and requires custom payment flows, Stripe is a great choice, but expect a more complex setup.
- If you run a retail store or restaurant, Square’s POS system is hard to beat, but you’ll need to manually sync sales with QuickBooks.
- If you process a lot of international payments, PayPal offers global reach, but can complicate your accounting due to its separate funds system.
At the end of the day, ease of use isn’t just about setup, it’s about how seamlessly your payments integrate with the rest of your business.
Integrating Other Payment Processors with QuickBooks
At MISSION Accounting, we always recommend QuickBooks as your go-to accounting software, and for good reason! It’s designed to streamline financial management, automate invoicing, and provide real-time insights into your cash flow. Plus, when you use QuickBooks Payments, transactions are automatically recorded and reconciled, eliminating the need for third-party connectors or extra manual work.
We also understand that some businesses prefer using other payment processors, whether it’s Stripe for e-commerce, Square for POS transactions, or PayPal for online sales. The good news?
You don’t have to sacrifice the power of QuickBooks to use these tools, they can all be
integrated with the right setup.
How QuickBooks Integrates with Other Payment Processors
- Stripe + QuickBooks – Stripe doesn’t natively sync with QuickBooks, but third-party apps like Synder or Zapier can connect the two, ensuring Stripe transactions are automatically imported into QuickBooks.
- Square + QuickBooks – QuickBooks offers a Square Connector, allowing sales data from Square POS to sync directly into QuickBooks Online. However, it still requires regular review to ensure accurate categorization.
- PayPal + QuickBooks – QuickBooks integrates with PayPal through PayPal Sync or third-party tools, but managing PayPal transactions in QuickBooks can still be tricky due to how PayPal holds funds before transferring them.
Related Reading: My 5 Top Must-Have QuickBooks Apps
What You Need to Watch Out For
While these integrations make life easier, they aren’t always seamless. We’ve seen clients run into data duplication, incorrect categorization, and reconciliation errors, which can cause major headaches down the line.
That’s why having the right integration setup from the start is critical!
Need Help Getting Set Up? Let’s Make It Easy
Choosing the right payment processor is just the first step, making sure it integrates correctly with QuickBooks is what really matters. MISSION Accounting helped countless businesses set up QuickBooks Payments, Stripe, Square, and PayPal in a way that eliminates manual work, prevents accounting errors, and keeps their financials running smoothly.
Our team specializes in seamless payment integration, ensuring that transactions sync accurately and efficiently with your books. Whether you’re looking to automate invoicing, streamline reconciliation, or connect multiple payment platforms, we have the expertise to get it done right.
If you’re not sure whether your payment system is working for you or creating more headaches, let’s talk. Schedule a free consultation today, and we’ll help you set up a system that saves you time, improves cash flow, and keeps your finances on track!
