Note: This article covers freee, a cloud accounting software service specific to the Japanese market. The information below will not be directly relevant if you are not selling in Japan or do not use this Japan-specific service.
Many merchants running a Shopify store find bookkeeping and accounting work burdensome. For those merchants, we explain the benefits and setup steps for integrating the cloud accounting software "freee Accounting" with Shopify. If you want to streamline your bookkeeping and accounting operations, please use this article as a reference.
What is the cloud accounting software "freee Accounting"?

Image source: freee Accounting
"freee Accounting" is Japan's largest cloud accounting software. It lets you manage bookkeeping tasks such as billing and payments, as well as accounting tasks such as ledger and financial statement preparation, all in the cloud, greatly improving operational efficiency.
Some people may feel uneasy about managing important company information in the cloud, but freee has robust security, including strong authentication and encrypted communications.
We explain in detail what freee Accounting can do and its pricing plans.
Covers all the functions you need for accounting
freee Accounting comprehensively covers the following functions needed for accounting and bookkeeping.
- Journal entry input and ledger creation
- Preparation of financial statements
- Creating quotes and invoices
- Expense reimbursement processing
and more
It supports not only corporate financial closing but also tax filing for freelancers and sole proprietors.
Automation of journal entry and data input work
freee Accounting can connect with bank accounts, credit cards, and even e-commerce services, allowing you to automatically import transaction data. You can also scan receipts and invoices to have them read by AI.
This kind of automation greatly reduces tedious journal entry work and manual data entry.
Creating management analysis reports
freee Accounting lets you check the day-to-day flow of money in your business (sales, expenses, profit status, etc.) in real time.
You can also display profit and loss by department and generate cash flow forecasts, allowing you to analyze your company's business performance from various angles.
Since the data can be checked clearly in graphs and tables, it can be used as-is for decision-making material in management meetings or reports to financial institutions.
Supports the Electronic Books Preservation Act and the invoice system
The Electronic Books Preservation Act (commonly known as "Denchoho"), which sets rules for preserving electronic data such as ledgers and transaction documents, ended its grace period on December 31, 2023, and electronic transaction data must in principle now be preserved electronically.
In addition, the qualified invoice retention system (commonly known as the "invoice system"), which started on October 1, 2023, is a system related to consumption tax input deductions that corresponds to multiple tax rates, and it has various effects on accounting operations.
freee Accounting supports these recently introduced accounting-related laws and systems as well.
freee Accounting pricing plans
freee Accounting's pricing plans differ for corporations and sole proprietors. This article mainly explains the corporate plans. To check pricing for sole proprietors, please refer to the product page for sole proprietors.
| Plan name | One-Person Corporation | Starter | Standard | Advance | Enterprise |
|---|---|---|---|---|---|
|
Annual fee *Monthly payment also available |
¥35,760/year | ¥65,760/year + usage-based fee |
¥107,760/year + usage-based fee |
¥477,360/year + usage-based fee |
Contact for pricing |
| Features | ・Basic ledgers and financial statement creation ・Purchase order/quote document creation, electronic document management ・Minimal management reports ・Full support for the invoice system and Electronic Books Preservation Act ・1 member |
・Basic ledgers and financial statement creation ・Purchase order/quote document creation, electronic document management ・Management analysis reports ・Full support for the invoice system and Electronic Books Preservation Act |
・All Starter features ・Custom reports ・2-tier department settings ・Custom permissions ・Group management ・Monthly closing and other control features |
・All Standard features ・Accounts receivable/payable management ・Expense reimbursement ・Workflow features ・Management accounting and budget-actual management ・Enhanced control features |
・All Advance features ・Internal controls at listed-company level ・Enhanced security ・Advanced fixed asset management |
- Usage-based fee | ¥107,760/year
- Usage-based fee | ¥477,360/year
- Usage-based fee | Contact for pricing | | Features | ・Basic ledgers and financial statement creation ・Purchase order/quote document creation, electronic document management ・Minimal management reports ・Full support for the invoice system and Electronic Books Preservation Act ・1 member | ・Basic ledgers and financial statement creation ・Purchase order/quote document creation, electronic document management ・Management analysis reports ・Full support for the invoice system and Electronic Books Preservation Act | ・All Starter features ・Custom reports ・2-tier department settings ・Custom permissions ・Group management ・Monthly closing and other control features | ・All Standard features ・Accounts receivable/payable management ・Expense reimbursement ・Workflow features ・Management accounting and budget-actual management ・Enhanced control features | ・All Advance features ・Internal controls at listed-company level ・Enhanced security ・Advanced fixed asset management |
*As of December 2024 *Users of legacy plans will be migrated to the above new plans starting January 15, 2025.
As shown above, pricing varies depending on your company's size and the features you use. Since freee Accounting offers a 30-day free trial, we recommend checking which plan is the best fit for your company's accounting processes.
Benefits of integrating Shopify with freee Accounting
Shopify can be integrated with freee Accounting. The benefits of integration are as follows.
Reduced bookkeeping work
Depending on the store, an e-commerce site may receive dozens or even hundreds of orders per day. There simply isn't enough time to manually record sales and expense management for each one, one by one.
By integrating Shopify with freee Accounting, order data is automatically synced, reducing bookkeeping work.
Prevention of input errors and omissions
No matter how careful you are with manual entry, it's difficult to eliminate human error entirely. If a serious mistake occurs due to input errors or omissions, it could have a severe impact on business operations.
Automated processing by machine minimizes human error.
Shopify and freee Accounting can be integrated via an app
Shopify and freee Accounting can be integrated using "Easy freee Accounting Data Integration," an app available in the Shopify App Store.
Shopify and freee Accounting integration app: Easy freee Accounting Data Integration

Image source: Easy freee Accounting Data Integration | Shopify App Store
"Easy freee Accounting Data Integration" is a dedicated app for integrating Shopify with freee Accounting, allowing you to automatically sync order data with a simple setup.
There are four plans, and the differences are as follows.
| Plan name | Light Plan | Basic Plan | Advance Plan | Enterprise Plan |
|---|---|---|---|---|
| Monthly fee | $14 | $29 | $49 | $99 |
| Monthly bookkeeping entries | 50 entries | 200 entries | 600 entries | Unlimited |
| Overage fee | $0.30/entry | $0.15/entry | $0.05/entry | - |
| Past order sync | Up to 1 month back | Up to 3 months back | Up to 6 months back | Unlimited |
| Features | ・Automatic/manual sync | ・Light Plan features ・Additional settings for vendors, discounts, etc. |
・Basic Plan features ・Inventory count journal entry support |
・Advance Plan features ・Dedicated customization ・API |
*As of December 2024
An overage fee applies per entry for bookkeeping entries beyond the monthly limit.
Only the Light Plan offers a 7-day free trial. While functionality is limited, it should be enough to get a feel for using the app.
Steps to integrate Shopify with freee Accounting
We explain the integration steps using "Easy freee Accounting Data Integration."
STEP 1. Register a freee Accounting account
If you don't have a freee Accounting account, register for one first. freee Accounting offers a 30-day free trial, so if you're interested, we recommend trying it out first.
You can register an account from the official page.
STEP 2. Install the app and select a plan
Install "Easy freee Accounting Data Integration" from the Shopify App Store.

Image source: Easy freee Accounting Data Integration | Shopify App Store
An installation confirmation will appear in the Shopify admin. Click "Install."

Image source: Shopify admin
Once installation is complete, the plan selection screen will appear. Select a plan and click "Approve" at the next billing section.

STEP 3. Connect the app with freee Accounting
After approving the plan, the freee Accounting connection screen will appear. Click "Connect to freee Accounting."

Log in to freee Accounting. If you're already logged in on the same browser, the account login step will be skipped.

Image source: freee Accounting
If the access permissions and business (company name, etc.) being accessed are correct, click "Allow."

The "Select business" screen will appear. Select the relevant business and click "Select."

This completes the integration between your Shopify store and freee Accounting.
STEP 4. Initial setup
Once the integration with freee Accounting is complete, configure the initial journal entry settings. The main items to configure are as follows.
- Mode: Choose whether to record Shopify Payments transaction fees. In general, select "Mode with transaction fees."
- Account item: Choose which account item to record Shopify sales under. In general, select "Sales revenue."
- Transaction fee settings: Select the account items for transaction fees, adjustment amounts, and refund amounts.

That completes the initial setup. If you have a tax accountant, we recommend sharing and confirming the account item settings with them.
Precautions when integrating Shopify with freee Accounting
Please note the following points when integrating Shopify with freee Accounting.
Restrictions based on the app plan
Journal entries and account items may be processed differently depending on the company. If you want to change the default settings for shipping fees, discounts, or consumption tax, you'll need to upgrade to the Basic Plan or higher.
The number of items and departments you can configure, and whether registration to transaction memos is available, also vary by app plan.
When trying to configure the optimal settings for your company, you may find you need to upgrade to a higher-grade plan, resulting in unexpected costs. Be sure to check this in advance.
Handling cancellations and returns
If a Shopify order is cancelled or returned, it will not be automatically recorded in freee Accounting. You'll need to take one of the following two actions.
1. Delete the relevant order in freee Accounting
2. Process the cancellation/return order in freee Accounting
Since these irregular situations may not sync automatically, please check regularly to avoid missing any bookkeeping entries.
Integrate Shopify with freee Accounting to reduce the burden of bookkeeping and accounting work!
This article explained the benefits and integration method for connecting the cloud accounting software "freee Accounting" with Shopify.
When your business is small, bookkeeping and accounting work isn't much of a burden, but as orders increase, it becomes a very significant one.
Use this information to reduce the burden of bookkeeping and accounting, freeing up resources for the important work you should really be focusing on, and grow your business.
Lastly, the blog article below introduces recommended apps that help streamline your operations. Please use it as a reference.
