How to do Shopify accounting when using multiple Shopify payment methods

How to do Shopify accounting when using multiple Shopify payment methods

What makes Shopify accounting special for thousands of e-commerce businesses? First of all, it is the option to connect several payment gateways to your online store. Secondly, the ability to accept Shopify POS and manual payments in addition to online orders. This makes purchases extremely convenient for customers. But for merchants, using multiple Shopify payment methods at once becomes challenging in terms of bookkeeping. 

The good news is that this problem has a simple solution. Whether you are using Shopify Payments or connect a variety of third-party payment gateways, like PayPal, you can account for all your Shopify orders correctly. Want to know how? This article will tell you.


Best Shopify Accounting Software

Shopify QuickBooks Integration

Accounting for Shopify POS and Shopify Manual Payments

Shopify Payments vs. Other Shopify Payment Processing Optionss

Best Payment Gateway for Shopify

Best Shopify Accounting Software

When you are choosing accounting software for Shopify, keep in mind that it should have certain useful features.

It should be able to do the following:

  1. Process Shopify POS and Manual Payments. If you want to export Shopify orders from the POS terminal or enter them manually, the accounting software should have additional settings to process these types of data.
  1. Gather data from all payment providers that you connect to your Shopify store. There are several ways for customers to pay online, without using a credit card or Shopify Payments, like PayPal and AmazonPay. Your software needs to import transaction data from all payment gateways accurately and not create duplicates in accounting.  
  1. Correct accounting for Shopify fees. You can be charged several transaction fees for online transactions, depending on your country, Shopify subscription plan, and other third-party payment provider fees if you use them. Other expenses should be taken into account too, like Shopify sales tax and shipping.

Synder performs all these functions without errors. It is a smart accounting product that integrates e-commerce, payment, and accounting platforms seamlessly. This software streamlines financial data flow and provides easy accounting without discrepancies. 

Let’s see what it can do for your Shopify store.

Shopify QuickBooks Integration

Understanding Shopify payment processing is an important step towards selecting the right accounting solution for your business. For example, if you use Shopify Payments, you won’t see transactions in QuickBooks right away. Shopify provides financial data only after you receive payouts (transfer of funds to your bank). It can take a few days for the funds to appear in your bank account. That’s why the integration software that knows how to gather data in the right way is essential for healthy e-commerce bookkeeping.

Synder is a flawless solution for Shopify QuickBooks integration. Once you connect Shopify to QuickBooks via Synder, the software imports all your sales details into accounting in the correct way. 

Here’s how it works:

Benefits of using Synder

  1. Synder automatically creates a Clearing Account in your Chart of Accounts in QuickBooks where it stores all details from your Shopify orders in one place. 
  1. Once money payout happens, Synder makes a transfer to your checking account for easy reconciliation. From now on your Shopify orders will be synchronized to the Shopify Bank Account.
  1. Thus, all your most important information — Shopify orders, Shopify inventory, Shopify customers, and Shopify shipping — receive an automatic update. 
  1. Shopify fees and sales taxes become easy to account for, too. Synder allows using the Apply taxes setting to recognize tax details in each Shopify sale and record them in QuickBooks.
  1. In addition, Synder can import historical data from your Shopify account too if you need it. 

How to connect Shopify to QuickBooks via Synder

Ready for integration? In this video, our expert explains how to connect your Shopify store to QuickBooks accounting using Synder in a few quick and simple steps. 

Please, enjoy! 

Accounting for Shopify POS and Shopify Manual Payments

Synder can easily account for Shopify POS transactions and orders entered manually too. All you need to do is select them in the settings of your Shopify company in Synder. As simple as that!

What is Shopify POS?

Shopify POS is a point-of-sale app that allows you to sell products in person. It is a great addition to online sales to many merchants. You can use Shopify POS to sell almost anywhere, including brick-and-mortar stores, markets, and pop-up shops. That’s why you might want to use it for your business too.

Synder works with Shopify POS orders without a hitch:

  • Once you adjust the settings and allow Synder to “see” your POS orders, the software synchronizes them right into your QuickBooks. Historical data import is available for your POS transactions too. And Synder automatically synchronizes newly created POS orders by default settings. 

If you want to learn more details, please check this guide on Shopify POS synchronization by Synder

Specifics of Shopify Manual Payments

Some customers don’t want to pay for their orders using a credit card. Shopify allows merchants to sell to such customers by setting up a manual payment method. Common types of manual payments include cash on delivery (COD), bank transfers, or, for example, you can send an invoice to your customer. 

Orders that accept manual payments are marked as unpaid on the Orders page. After you receive the payment, you must manually approve the order.

This process can make gaps in bookkeeping. But Synder will help:

  • When you select Manual Orders in your Shopify company in Synder, all transactions entered by you manually in Shopify will be accounted for just like any other. With no errors or discrepancies.
  • What is more, if you synchronized manual orders in Shopify and they got refunded, you can easily update these transactions in Synder to keep accounting in order. Visit our guide on refunds for Shopify Manual Payments to learn more.

Shopify Payments vs. Other Shopify Payment Processing Options

Shopify gives online sellers an option to accept payments from different payment providers. You can use Shopify Payments, a native Shopify payment gateway. There are also several ways for customers to pay online without using a credit card, like PayPal and Amazon Pay, for example. 

The variety of Shopify payment processing options can become both a great growth opportunity and a challenge to e-commerce business owners. 

The automation software will need to gather data from each payment provider separately but account for them in one place. And of course, be able to achieve accurate reconciliation at the end of each month and keep your books in order.

Is it possible?

With Synder, it is.

Organizations feature in Synder allows you to connect each payment gateway, no matter how many of them you use, separately to your Shopify company in Synder. Then the software will accurately extract financial information from each source and record it in QuickBooks with precision. 

With Synder, data from Shopify Payments and other payment processing companies will supplement each other without duplicates and errors. Even if you use a payment processor that is not on our integration list, it’s not a problem. You can migrate any data to Synder through Excel at any time. You can be free to use as many payment gateways as your Shopify store needs. 

What is Shopify Payments?

Shopify Payments is the simplest way to accept payments online. It eliminates the hassle of setting up a third-party payment provider or merchant account and having to enter the credentials into Shopify. Your customers can complete their purchases directly on your online store without having to pay at a third-party checkout.

You are charged transaction fees each time a customer makes a purchase using a third-party provider. To avoid transaction fees, you can activate Shopify Payments instead.

Other Shopify Payment Methods

If you’re using an external provider, your customers must complete their purchases on a checkout page that’s hosted outside of your online store.

You can activate or change a payment provider from the Payments page of your Shopify admin.

When you set up a payment provider to accept credit card payments, each payment must be processed, so there is usually a delay between when the customer pays for their order and when you receive the payment. After the payment is processed, the purchase amount will be transferred to your merchant account.

If your Shopify store accepts payments via different channels (e.g. PayPal, Stripe, etc.) you need to connect these payment platforms to Synder as well for the app to recognize all transactions and sync them successfully. Just click the Plus icon in the top-right corner and follow the already familiar steps. This will allow Synder to record Shopify fees amounts into your accounting company.

Best Payment Gateway for Shopify

Shopify PaymentsThird-party payment gateways 
Simple set-upMore flexibility in payments
Quick check-out for customersAttract more customers
No extra transaction fees Increase trustworthiness in your Shopify store
Chargeback feesCustomers redirected to complete checkout
Funds can be frozen for suspicious activityExtra transactions fees
Not for every countryCan have other additional restrictions

Shopify PayPal Integration

When it comes to third-party payment providers, PayPal is one of the most popular options Shopify sellers and buyers prefer. If you run a Shopify business, you might want to consider PayPal integration too.

Why do people choose PayPal for their Shopify stores?

The first thing to mention, PayPal is one of Shopify’s default payment providers. That’s why you can set up Shopify pay with PayPal in less than a day. As soon as you open a store, you get a PayPal Express Checkout account activated with any of your Shopify packages. Using PayPal with Shopify also offers functionalities like easy cart integration, multiple customization options, online invoicing, and facilitates credit card payments over the phone. Over 220 million active PayPal users globally come as a pretty great bonus of this payment provider as well.

No wonder, PayPal opens the top of alternative Shopify payment processing options.

How to account for PayPal transactions as your Shopify payment provider

Usually, to account for PayPal transactions, you have to create a bank type account for them in your QuickBooks and then enter your PayPal sales and expenses transactions manually. 

Another popular option would be to export all PayPal transactions to Excel sheets and use importing apps to get them to QuickBooks faster.

However, both of those options require a lot of manual work to do. There is a better solution that can save you hours. Moreover, the whole process will be totally automated!

You can easily connect PayPal to your Shopify company using Synder software. It helps data flow smoothly into your QuickBooks system. With just a click, you can achieve error-free reconciliation for all your Shopify sales that were paid via PayPal. 

All PayPal transaction details, including processing fees, get recorded and accounted for correctly. Start saving time now! Synder is free to test.

Key Takeaways

E-commerce businesses have special needs when it comes to bookkeeping. Multiple payment processing options and different platform fees make calculating the net income amount in your bank difficult. 

The Shopify QuickBooks integration provided by Synder allows importing payments into accounting software, synchronization, and categorization of data in your books with incredible accuracy for a perfect reconciliation process.

You can enjoy the benefits of using multiple Shopify payment methods without the fear of discrepancies in your accounting:

  • Shopify POS
  • Shopify Manual Orders
  • Shopify Payments
  • Third-party payment gateways
  • Shopify PayPal integration

All these options can easily become a source of increased cash flow to your e-commerce business. With the seamless Shopify QuickBooks integration that Synder provides, your bookkeeping process will always be effortless and trouble-free.

Olga Shvets

Olga Shvets

Olga is a FinTech writer with a degree in communications and business experience in e-commerce. Passionate about all things connected with money and the principles of human behavior. Financial psychology and trends of global markets are her favorite topics to investigate.

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