Managing Accounting for E-Commerce Clients With Synder

Synder Business & Accounting Blog
6 min readOct 23, 2020


An overview of the most common issues and the ways to solve them.

If you have ever spoken to an e-commerce accountant or a bookkeeper about their workload, the amount of time they have to spend on managing online transactions coming from different sources most likely made you anxious. It happens because compared to other businesses, who might only have one business account, online stores can accept payments via as many as ten different channels, all of which need to be accounted for.

However, the very nature of e-commerce brings a silver lining to all of us striving to be more productive: it has a very direct potential for automation. Since transactions take place online, there shouldn’t be a reason why they can’t be automatically recorded in accounting software, such as QuickBooks or Xero, paving the way for producing accurate financial statements. Yet, among the accountants, there is still a lot of frustration with solutions that are unable to fully automate what needs to be automated.

This article will outline some of the main problems connected tosynchronizing online payments as well asways to solve them.

What is Synder: an overview
Synder is a solution that has been built together with leading QuickBooks and Xero accountants. It takes highly important, crucial points specified by the professionals in the field into account to provide a professional solution, focused on detail and precision.Synder allows accountants and SMBs to synchronize e-commerce transactions from Stripe, PayPal, Shopify, and other payment and e-commerce platforms with QuickBooks Online, QuickBooks Desktop, and Xero. A wide range of advanced configurations (accounting for shipping, assigning classes to income transactions and expense categorization, discounts, tips, fees, correct tax filing) is available to record transactions with maximum details. A dedicated and knowledgeable live support team is available to assist.

Syncing online payments with QuickBooks and Xero. Main issues accountants face

Many popular market solutions that bring in e-commerce data from PayPal, Stripe, Shopify, and other payment and e-commerce platforms, simply do not properly work with processor fees that make up an important part of every online transaction. Most solutions don’t allow accountants to choose an account where they would like the fees to be recorded, and, what is probably the worst thing for accountants because of it the net income amount usually isn’t accounted for. The processor fee is already deducted. That makes producing an accurate income statement nearly impossible and reconciliation incredibly difficult.

Most solutions struggle with processing the refunds that occurred in payment and e-commerce platforms. In e-commerce accounting, it means hours of manual processing, and many discrepancies can occur because a sales transaction has been recorded, a fee has been accounted for, but the refund of the total amount has not been processed.

Categorization is another extremely valuable point that has to be automated by any solution aimed at optimizing the bookkeeping process and yet, it is overlooked by most software providers.

Many business owners will want their sales auto-categorized based on products. Not all payment processors store all necessary data, but another issue is that very often the solutions accountants work with are unable to work even with the information given. As a result, individual products are often sent over to one generic product category. Dealing with that is an issue, and should be automated to the largest extent possible.

The previous pain points already make it very difficult for accountants and bookkeepers to manage what really should be automatically recorded in QuickBooks or Xero. There are third-party apps and native solutions that deal with some of these pain points. However, the absolute majority of them only focus on one or two payment or e-commerce platforms. For any accountant or a bookkeeper with a sizable practice that means hours and hours of work, going from one individual file to another, and managing everything in separate accounts.

Responding to the main issues

Today, we are going to look at Synder as a solution designed to automate the bookkeeping of online transactions from many sources with a high level of customization and detail. With it, you can manage e-commerce transactions from different platforms in one place. This perfectly suits accountants with a large practice, because with Synder they can connect many QuickBooks/Xero files to their single profile.

Let’s take a look at some of the answers to the most pressing needs of accountants and bookkeepers working with e-commerce clients.

Accountant-level of detail

Because Synder has been developed in collaboration with leading accountants, it includes absolute must-have features, such as:

  • Correct accounting for the fees — a sales receipt/invoice payment with a full amount, including the fee, is created in the accounting system automatically. A separate expense transaction is created to reflect the payment platform fee, making a simple, transparent reconciliation a given.
  • Accurate recording of refunds.
  • Smart categorizations to automate this process as much as possible.
  • A number of advanced settings designed specifically for accountants to cover the most nuanced business needs from recognizing different locations and recording the tips to fine-tuning tax settings when possible, and much more.

Highest level of accuracy

Because transparency and security are perhaps the most important factors for e-commerce businesses, Synder is equipped with a highly-secure Rollback function — a must for any such software that is not always a given. The Rollback feature allows an admin to securely undo any sync, giving accountants peace of mind and an ability to have full control over a completely automated process.

Duplicates aren’t allowed to go through, and a highly secure rollback option allows accountants to have a full visible dashboard with all of the app’s activity, as well as a one-click ability to completely undoany action.

One app. Many platforms supported

Accountants are able to open their profile and securely connect all of their clients’ files, as well as their respective payment and e-commerce platforms. As of October 2020, QuickBooks Online users can connect up to 8 different platforms, and new integrations are constantly added for QuickBooks (both Online and Desktop) and Xero users.

Your clients will appreciate the security of the process, as accountants do not require access to their sensitive payment platform login data. An account can be linked by its owner using an invitation sent from the accountant, who can take care of the rest.

The pricing

The Synder pricing is also very accountant-friendly, as subscribers can connect an unlimited number of companies,and pay only for the number of transactions they process.


We have touched upon the most relevant issues for professional accountants who manage e-commerce transactions. There are many other important questions that some accountants or bookkeepers face, such as recording details for products sold (Synder makes tracking the inventory easy thanks to its detailed syncing of sales data), keeping track of customer info on sales receipts, recording transactions with different currencies, and more.

These features are also supported by Synder, but in this particular case, we wanted to focus on the most burning issues, as the dichotomy between small businesses increasingly switching to accepting payments online and the tedious work of recording these transactions makes it a pressing issue.

Related: Learn about 4 Killer Synder features every CPA should try.

Sign up for a free trial (no credit card required) and reach out to the Synder support team using the in-app chat or the contact data in the footer of this page to learn more about what Synder can do for your practice.

Originally published at on October 23, 2020.



Synder Business & Accounting Blog

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