7 Best Shopify Accounting Software In 2022

In all possibility, you find Shopify’s inbuilt accounting module/system lacking the teeth required to manage the complex financial data that your business generates.

You are not alone.

Many ecommerce brands tend to veer towards third party accounting software.

Because right accounting software helps businesses track their income and expenses, generate reports in a few clicks, prep for taxation, manage sales tax by location, send invoices and receive payments, to name a few.

Shopify is a powerhouse at order management. But when it comes to managing cash flow, it leaves a void.

Our team has analyzed the best accounting software for Shopify stores in 2021. Based on our research, we have curated a list of the best options.

Let’s dive in.

What are the Best Accounting Software?

Here are our top picks of the best accounting software for Shopify to try this year.

1. QuickBooks Online

Quickbook online- Best shopify accounting software

QuickBooks Online has fast become one of the most popular accounting software for small and mid-sized e-commerce stores. The brand name is Intuit QuickBooks and it also earns the distinction of being one of the oldest brands in the accounting business, given that it was set up in 1984.

QuickBooks online is a feature-rich option. It boasts of over 200 integrations, inventory management, multiple invoicing modules, payroll management & currency options. Here’s a look at the key features for Shopify Stores.

Key Features:

1. Well-designed Dashboard

QuickBooks offers an information-rich dashboard with a friendly user interface. You will not miss on any important details at a glance. But you won’t get lost in the noise either.

2. Customer Management

QuickBooks has an advanced customer management module that allows you to store vast customer details for future use.

Default payment options, tax codes, addresses, contact names and the option to email multiple customers at the same time.

3. Live Bank Feeds

QuickBooks simplifies bank reconciliation. Unfortunately, they did away with their duplicate transaction detection feature in the recent update. But even then, it’s pretty easy to define rules, track expenses & organize expenses further.

4. Real Time Updates

Whenever there’s a sale, the item quantities are automatically updated in QuickBooks. Also, we like the fact that when you import order and refund data, you also get sales tax data with it.

5. Tons of Reporting

You can generate a plethora of customizable reports on your finances. This is plan specific though. The Simple Starter plan allows you to generate 27-reports. This jumps up to 75-reports on the Plus Plan.


QuickBooks Online has a basic subscription, called the Simple Start Plan at $12.50/month. This has all the features for small ecommerce businesses.

Then there’s the Essentials Plan $20/month.

The Plus Plan at $35/month & the Advanced Plan at $75/month.

The advanced plans bring more capabilities to the table, such as adding up to 25 users, a dedicated account team and automated workflows.

2. Xero

Xero is undoubtedly one of the most widely used accounting software in the ecommerce industry. This is a fully-loaded software suite that manages everything under the wide accounting umbrella. You have tons of automations, more than 160 currency choices, POS software integrations, bookkeeping and even marketing.

With Xero, even large businesses won’t be left craving for more features. It has all the bells and whistles one needs to seamlessly manage ecommerce finance without getting bogged down under a burden of numbers.

Key Features:

1. Dynamic Dashboard

The Xero Dashboard is eye-pleasing and information rich. The UX is easy to navigate through. Businesses can track most important details without probing deeper into hidden layers. There are graphs, unpaid invoices, claims and bank accounts, all neatly stacked for your convenience.

2. Reports Galore

Reporting is where Xero tides over the competition. The software lets you generate 65 reports. Each one of them is as comprehensive as you need it to be.

Basic balance sheets, depreciation schedules as well as detailed budget reports can be generated. If you frequently generate a particular report, you can mark it for easy access.

3. Payroll Management

We really liked the payroll management module. It makes it effortless to track employee earnings, altering payment schedules and keeping track of sick leaves as well as paid leaves. This feature is limited to users in selected countries though.

4. Invoicing

The invoicing system is exhaustive. You can generate bulk invoices, recurring invoices & set default payment options. The invoice template is limited to one, in comparison to the 5 that QuickBooks offers. That said, you can upload a custom invoice. So that’s not a deal breaker in our humble opinion.


Xero offers three plans. The Early plan at $11/month is perfect for startups, small businesses and one-man operations. It doesn’t offer multiple currencies though.

There’s the Growing Plan at $32/month for small businesses, which again lacks this feature. The Established Plan at $62/month is the fully-loaded option.

3. Sage Business Cloud Accounting

Sage Business Cloud Accounting

Sage Business Cloud Accounting which was formerly known as Sage One is a feature-rich, yet simple online accounting software for small businesses.

Sage offers numerous business-specific solutions, mind you. We will limit our discussion to the Cloud Accounting software though, because it is one of the most popular choices amongst ecommerce stores.

Besides, it boasts of one of the most affordable price tags industry-wide. That can be a huge motivator, especially for startups who are testing the waters with ecommerce.

Key Features:

1. Connectivity

Sage is a cloud-based accounting system. This allows seamless connectivity from any part of the world. You are not shoehorned into accessing the system from one device or a single geo. You can download their mobile app and upload business data when you are travelling.

2. Automation

While there are tons of features on offer, the one that separates Sage from the rest is ‘Automation’. If you are a small business or a freelancer without the capital overheads to hire fulltime staff, this module saves you tons of time and money.

You can automate most of the repeated tasks. Sage can automatically generate invoices, quotes & business reports. You will no longer have to waste critical time updating transactions yourself.

3. AI Powered

Sage uses AI and machine learning to automatically detect your inputs, which allows the software to adapt to them. In simple terms, more automation.

4. Loaded Dashboard

The Sage accounting dashboard gives you a holistic view of the cash flow. You can track expenses, orders, pending payments, canceled orders and invoices, to name a few. A few clicks allows you to quickly generate reports for each one of these.


Sage Accounting has a starter plan at just $10/month. It offers invoicing, cash flow tracking and automatic bank reconciliation. Terrific for small ecommerce merchants. The fully stacked plan starts at $25/month. But depending on where you are, you may be able to avail huge discounts, or even get a three-month trial.

4. NetSuite

We have been looking at the best Shopify accounting software for small and medium-sized businesses. Here’s NetSuite, an enterprise resource planning (ERP) system that’s used by more than 40000 businesses in 160 countries. It’s a cloud-based system that’s offered as a software-as-a-service (SaaS).

While it is not a pure accounting software, because its capabilities are exhaustive, it is one of the most feature rich options for large brands, who may find smaller business solutions lacking. If there is anything accounting-related, you can be rest assured that NetSuite offers it.

Besides, the software offers ample customization allowing you to tailor it based on business type and industry.

Key Features:

1. Massive Dashboard

Depending on your subscription, NetSuite shows you brief summaries of all key metrics related to your ecommerce operation. Each one of these is expandable. NetSuite calls it a ‘Portlet’, which is a portmanteau of the words ‘Portal’ & ‘Inlet’. In other words, each portlet is an inlet into a portal of its own.

You can see invoice data, KPIs, customer data and other metrics and dig deeper into each. Also, this display is role-specific. So, the accountant would see a different dashboard from the CEO.

2. Revenue Recognition

NetSuite can make it easy to ensure compliance with accounting standards like ASC 605 & IFRS 15. The framework is a rule-based one that allows businesses to automate auditing, reclassification & forecasting, to name a few tasks.

3. Reporting

NetSuite relies on vast amounts of data to make precise revenue forecasts. Businesses can use real-time data analytics to develop budgets and preempt worse case scenarios.

While the sheer amount of features on offer is huge, NetSuite is designed to perfection. You will never be too far from a one-glance view of the finances, which makes it easy to come to prompt decisions.


NetSuite is priced at $999/month with an additional $99/user. This of course is the base price. The actual monthly cost will vary significantly depending on your business needs. That looks steep. But don’t forget that this is not merely an accounting tool. It’s an ERP system that can manage the entire business more efficiently.

5. Botkeeper

Botkeeper Accounting

Botkeeper is an innovative addition to this list of best Shopify accounting software. For starters, it’s an AI-powered accounting system that relies on advanced, machine-learning algorithms to identify and adapt to your business.

Secondly, it lets you utilize its team of skilled, remote-working professionals and automate almost every accounting task. This is a hands-off approach to business, which a lot of ecommerce brands seek.

Moreover, we are talking about computer-controlled bookkeeping which translates into faster processing times and fewer errors. Despite all the fancy talk about automation and ease of use, accounting software in general are not easy for a layman to get hold of. Botkeeper changes that.

Key Features:

1. The Dashboard

Botkeeper uses an interactive dashboard. By interactive, we mean that the machine is closely trying to learn every action you take, in order to automate it for you.

We love the user friendly layout. All the KPIs are clearly visible. You also have the option to completely customize this with widgets that use your data sources.

Each widget can have predefined goals. All-in-all, it’s the perfect 360-degree view of the financials.

2. ScanBot

Botkeeper is also available as a mobile app. ScanBot expands on the mobile capabilities of the software by allowing you to scan an image and load the financial data off it. It can be an invoice or a receipt. The financial data will directly be loaded into Botkeeper. No more manual inputs.

3. Automatic Bookkeeping

Botkeeper is designed for error-free and fast accounting. The software automates most tasks including account reconciliations, generating reports & categorizing transactions. The best part is that everything will be reviewed by Botkeeper’s team of accountants before it gets a final nod.

4. Inventory Tracking

Once integrated with your online store, Botkeeper tracks every transaction and automatically updates inventory levels in the backend.

5. Custom chart of accounts

You can generate personalized finance statements with Botkeeper using your own accounting info.

6. More Features

In addition to this, Botkeeper can also manage payroll administration, receivables, fixed assets, credit reconciliation, month-end close (manual review), reports, & revenue recognition.


Botkeeper offers three pricing models to choose from. The basic package starts from $59/month and extends to $2,940.30/month when billed annually. This depends on the average monthly expense for your business.

The Pro Package starts from $459/month and extends to $3,340.30/month. Once again, the pricing is expense-specific.

The Advanced Package starts from $659/month & extends to $3,540.30/month.

P.S – Notable mentions that didn’t make this list are Wave – The Free Accounting Software (Additional charges for advanced features), FreshBooks (limited reporting), & Zoho Books.

Best Accounting Apps within Shopify

If you are looking for an Accounting app/plugin that you can quickly pick from the Shopify store and get going, we have a couple of great options for you.

Do remember that the features that these apps offer will be tepid in comparison to the extensive range that you get with third-party software.

However, many new ecommerce stores may find enterprise-grade software to be overkill. Instead, they find great value with some of these plugins.

1. Profiteer

Profiteer is a basic COGS accounting plugin that allows you to keep track of the cost of goods sold (COGS). As you’d be aware, the COGS is one of the most important metrics that will give you an overview of profitability, and your business’s financial status.

Profiteer makes it easy to get a bird’s eye view of this important metric. All the inventory and cost prices are stored within Profiteer’s dashboard. So each time you generate a sale, the software automatically updates vital financial metrics.

Key Features:

1. Variant-specific Cost Prices

Profiteer allows you to store the accurate cost price for each product variant in the store. So, your profitability and margins are never hidden beyond a smokescreen of irrelevant data.

A minor quibble that a lot of people seem to have with it, is that when you integrate your store with Profiteer, it automatically sets the value of each variant at zero.

You have to manually update this with the accurate price. If you have a store with tons of products and variants, this will be a tedious task.

2. Easy Reports

Profiteer allows you to quickly generate reports that show you the total sales, POS sales, and profit margins for each one. You can also filter this further by highlighting your bestsellers. The order reports will show you the exact cost price for each product and variant.

3. Inventory Value

Profiteer will show you the total cost of your unsold inventory at a glance. This is an important, but otherwise time-consuming accounting task for most ecommerce brands.

4. Automated Currency Conversion

Profiteer will automatically convert currency values to update your profit statement.


Profiteer has a subscription-based model with prices starting from $15/month. You can however enroll for a 3-day trial of the plugin to see if it works for your business. If you have a large store with more than 25000 SKUS, the pricing starts from $30/month.

2. SimplyCost

SimplyCost is another Shopify accounting app that makes COGS tracking easy. But along with this, it also offers a plethora of other features, which increases the value that it brings to the table.

For instance, SimplyCost automatically accounts for taxes, shipping costs and discounts while calculating profitability. This can be quickly downloaded in the form of easy-to-grasp reports. The big draw though, is the pricing. For what it offers, SimplyCost is hands down the cheapest option out there.

Key Features:

1. Auto-Calculates Payment Processing Charges

Generally, payment processing charges have to be manually deducted from the selling price. With SimplyCost, you can add your payment gateways pricing plans to the dashboard and it does the rest.

It automatically calculates the gateway processing fee for all orders that use PayPal or Shopify Payments. If you are not using Shopify payments, it can automatically calculate the Shopify Transaction fee for each one.

2. Expenses

You can add your expenses, such as your ad-spend from Facebook or Google Ads to the dashboard. It will automatically convert currency and add to your cost if you are running ads in a different country, from your Shopify store. You can add both, one-time as well as recurring expenses.

3. Reports

SimplyCost helps generate more data-rich financial reports as compared to what Shopify offers. For example, you can generate vendor profitability reports which lets you make important business decisions about sourcing. You can check for profitability according to the product type as well.


Like we mentioned a while ago, the pricing is too good for the features it offers. SimplyCost is priced at just $4.99/month. That’s it. This is the only plan and it includes all the features. No additional charges for big merchants or more SKUS.

How to Choose Best Shopify Accounting Software

Choosing the best Shopify accounting software is undoubtedly difficult. Most software out there offer similar feature sets, most of which may be overkill for your business. That’s why we have created this brief buying guide to help you with the selection process.

We use a simple checklist while evaluating any software/service for ecommerce merchants.

1. Does it Serve Your Intended Purpose

There are different reasons why an ecommerce merchant needs an accounting software.

For some, it is reporting.

For others, it’s compliance with accounting standards.

A software might have the fanciest feature list you have ever seen. But if it doesn’t serve the most basic purpose, then its not worth it.

So jot down a list of features you need. Your pain points. Then prioritize it by significance. Now select one that meets most of the priority list.

2. Is it Easy to Use

The idea of using accounting software is to simplify complex accounting tasks.

Does the software serve this purpose?

Is it easy to use?

Can you find everything you need on the dashboard?

Can you quickly generate reports?

Can you define user roles?

The last thing you need is to subscribe for a software and then hire someone else to help you use it.

3. Is it Affordable for YOUR Business

Affordability is subjective. Only you can know whether an accounting software is a cost-effective choice or not. While calculating this, take into account the time and effort that you’d invest in managing the finances, without it.

4. How Helpful is the Customer Support

Last but not the least, we prefer software companies with multiple, reliable support channels. Ideally, it should offer 24/7 support.

This may not be an exhaustive list of features to watch out for. But it does tick off all the important boxes.

To Sum it up

The primary advantage of using accounting software is to reduce effort and minimize errors. You will spend less time with data entry, which lets you focus on your core competencies. At the same time, software will make it easier to generate extensive reports for a variety of metrics that’s not possible with Shopify.

That sums up our list of recommendations for the best Shopify accounting software. We hope that it serves as a starting point for your research and helps you understand the key benefits of each brand.

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