Best Accounting Software for Shopify

If your Shopify store is already generating sales, the time is now to configure accounting software that you feel 100% sure about. With the right information, you can finally make a confident and informed choice on accounting software for your Shopify store. In this blog, we will introduce the best accounting software options for Shopify.

Best Shopify Accounting Software

Using this comprehensive guide from your friends at Flowify, you’ll get a detailed look at how the eCommerce accounting alternatives stack up, and you’ll learn exactly why and how our winner took the gold.

But before we dive into how the accounting software options for Shopify compare, it’s important that we’re transparent about our approach in analyzing and naming the #1 option for store owners like you.

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While there are many options for Shopify accounting software, we chose to review the big three best accounting software: Quickbooks, Sage, and Xero. These are the most commonly used accounting software systems among eCommerce store owners. In a few cases, we do reference two “runner-ups,” (Wave and Freshbooks) so that we can be fair to other platforms that do very well in certain categories. And although we didn’t include them, it’s important to note that we also considered Zoho Books and BrightPearl for the running.

xero dashboard flowify
Xero Dashboard

We’ve rated the top 3 Shopify accounting platforms based on Popularity, Performance, Reviews, and Price. There are many other considerations, however, so here are a few questions you’ll need to ask yourself before making a final choice on your accounting software for your Shopify store.

  • What software or tools does your existing Accountant / Bookkeeper use?
  • Are you ok with cloud computing instead of saving all the data on a local server?
  • Are there any industry standards or limitations to consider?
flowify man considering shopify accounting

Now that you’ve asked yourself the “tough questions,” let’s get on to the meat of our comparisons.


While popularity doesn’t always guarantee a premium product/service, when it comes to eCommerce’s best accounting software, being a big fish is important for a number of reasons, including:

  • Familiarity among accountants and bookkeepers is a must. If the software was not popular enough to have bookkeepers readily listing their competency with it, we didn’t include it here.
  • Get new features, faster. The big players roll out new features consistently and in a timely manner. For instance, new iterations and tweaks that make the software easier to use. This is for the benefit of the non-accountant (like you!).
  • If the company has earned the trust of loads of shop owners, you can bet they have a reputation to uphold, which can result in better customer service, updated features, and more innovative tech.
QuickBooks dashboard shopify accounting
QuickBooks Dashboard

Note: No accounting platform is worth the hassle if your professional accountant isn’t already familiar with it. A true pro has multiple clients, and likely won’t take the time to learn a new system for you, no matter how much they want to please you. So, if you’re working with an accountant or bookkeeper, be sure they get a say in which accounting software to use for your eCommerce store.

Popularity of Quickbooks for Shopify

QuickBooks popularity Ecommerce Accounting

Quickbooks Online is by far the most well-known and respected accounting software among accountants, with many thousands listing Quickbooks as their accounting platform of choice.

How do you account for the staying power of Quickbooks? They were among the first in the business, and have been consistently innovative over the years.

QuickBooks Mobile Shopify

It seems that Quickbooks has always been an accounting mainstay. Even though they aren’t always first-to-market (say, with cloud computing for instance), they almost always improve on what the competition creates, and they quickly train affiliates worldwide. Hence the domination.

We like that Quickbooks Online has an instant chat and phone number clearly listed on their front page where you can reach a real-life human being any time, for any reason. While we’ve heard that Quickbooks doesn’t offer the best technical help, it seems like they’re cleaning up their act in that regard.

Popularity of Xero for Shopify

Xero is a relatively big player in online accounting (though not even nipping at the heels of Quickbooks). They’ve been working hard to train accountants in their product. In fact, as of February 2019, Xero lists 444 “advisors” who are familiar with their products in the United States. The accountants and bookkeepers they list in the advisor directory each have at least eight clients on Xero, as well as staff members trained in Xero. As the software continues to grow, it will likely become a top choice for Shopify owners around the world.

QuickBooks Shopify Integration

Popularity of Sage50 for Shopify

Sage marketing ecommerce accounting

Sage 50’s approach seems a little more do-it-yourself. Rather than listing their affiliates outright, their website says, “Join industry peers, certified partners, and Sage pros online 24/7 in Sage City — the best place to ask questions as well as share product tips and tricks.” This is a novel solution, but leads us to wonder if all our accounting questions for our Shopify store must be self-directed.

There are plenty of reasons to choose one of the big guys for your Shopify store. However, popularity is just one of the factors that went into our decision making. Simply hopping on a bandwagon may be easy, but it’s not always wise.


Xero Online Accounting
Xero Online

We lined up these top three side by side to see how their most important features compare. We took a good look at the options for integrating the three accounting systems with Shopify.

If you sell products in more places than just Shopify, the ability to integrate your data and inventory while reducing manual work is necessary. And while there are lots of accounting systems to choose from, we needed the best accounting software that was more focused on product-based sales and handling inventory rather than simpler accounting solutions that were designed for service-based companies.

Sage mobile shopify accounting
Sage 50 on Mobile Phone

When grading performance, here were some of our considerations:

ecommerce accounting features
  • Shopify Integration was paramount. Any accounting solution that didn’t have an integration for Shopify was immediately eliminated from the running.
  • We wanted the Dashboard (your main hub) to be easy to use and intuitive in its design, because Shopify store owners are busy and just need things to work.
  • The Banking options had to be reliable and turnkey so that you can get real-time data.
  • Reporting should give valuable KPI’s at-a-glance, but also let you go deeper where needed. If reporting options weren’t plentiful, the overall score was significantly docked.
  • Customizations are important for Shopify store owners, especially as your number of SKUs increases. We think customizations should be readily available so that you’ll never feel needlessly limited.

We did our homework and determined that all three of our frontrunners, Quickbooks, Sage, and Xero have the features you’ll need as a Shopify user.  

Note: All three of these accounting platforms are accessible through the cloud, which means you won’t need to have your own server or IT pro. You don’t have to wrestle with setting up and finding space on your computer for it, it’s all done with a few simple clicks. And perhaps most counterintuitive, data is more secure when stored on the cloud.

So let’s see how they compare…

Quickbooks for Shopify Performance

QuickBooks accounting for shopify owners

Quickbooks immediately stood out as the most powerful accounting software option, with lots of room to grow. The dashboard can seem a bit complicated at first, but there are plenty of support options and how-to videos to help you along your way.

There are very clean banking integrations, and syncing of multiple money inflows can begin within just a few hours. We encountered no hurdles with record-keeping for Shopify stores, and with enterprise features at arm’s length, we knew we would want for nothing.

For Shopify store owners, Quickbooks performs like a well-oiled machine.

Xero for Shopify Performance

Xero for Shopify Performance
Xero Performance Features

We were impressed by the Shopify Xero inventory sync. Of all of the options for eCommerce store owners, Xero seems the best at helping you get in the door and putting what you need at your fingertips. But once your store starts taking off and you require more out of the performance of your Xero accounting system, you’ll need to start paying and paying handsomely. More on that in the pricing section.

Below you’ll see Xero’s dashboard is user-friendly and offers invoicing and inventory management.  

Xero Dashboard Accounting
Xero Dashboard

Sage for Shopify Performance

Sage prides itself on its Microsoft Office Integration and touts it as one of its best features. As Shopify users, we have to learn to see past what’s flashy and think about what is truly useful, like inventory management. And although we loved their tagging system, we found Sage’s reporting was not as robust as the other accounting options.

Sage Dashboard Shopify Accounting
Sage 50 Business Status Dashboard

Sage has a nice dashboard and great features for Shopify users.

One Sage reviewer writes:

“Major transactions are grouped together under tabs on the left-hand navigation panel. The various workflows–receivables, payables, inventory and services, employees and payroll, and a ‘company’ category–are all shown graphically. Each task within a major area is represented as a labeled icon, making it is to start a new transaction from this screen. The ‘company’ link is a catch-all category, including general journal entries, the chart of accounts, and tools for managing your data and accounting tasks.”


Sage Small Dashboard

Overall, we found that the features and performance offered by Sage are more geared to a professional accountant and less toward the time-strapped eCommerce store owner.

Honorable Mention: Freshbooks

Freshbooks is one of the accounting software options we had a soft spot for, but we determined it wasn’t a good fit for Shopify users based on some lacking performance features. Freshbooks is stellar for service-based companies, but we needed something more to help product-based eCommerce stores.


When choosing the best accounting software for your Shopify eCommerce store, reviews can be your biggest ally. But watch out! Fake reviews are a problem everywhere. And without a developer’s background, they can be hard to spot. We combed through what real Shopify users had to say about each of the three platforms and dissected their feedback on all available integration plugins.

Little Man Talking Icon

Here are some things we looked out for:

  • If a review was very short and revealed no understanding of the software product, it was not considered.
  • Reviews that seemed overly positive or negative without clear reasons were not counted.
  • Reviews that contained honest insight into what it’s like to use the system in real-life were given the greatest weight.

Quickbooks for Shopify Reviews

There is an important lesson here, and that is that no matter how popular Quickbooks is, your experience will only be as good as your Quickbooks-Shopify integration app.

QuickBooks own integration app for Shopify

You can see that Quickbooks offers its own integration app, but it gets terrible reviews (here, just two out of five stars). Don’t be discouraged though, sometimes you just have to keep looking!

We at Flowify are so convinced that Quickbooks is a great choice for Shopify owners that we actually took on the challenge ourselves, and we built our own Shopify-Quickbooks integration app, which you can try free for 7 days. Take a look here.

Xero for Shopify Reviews

We’re glad we read the reviews! While Xero seemed to be a clear frontrunner, the reviews on their Xero Shopify integration are very poor, with one reviewer describing it as “bookkeeping misery.” Otherwise, the reviews seemed generally positive for Quickbooks and Sage 50.

Xero App Shopify Review

Sage for Shopify Reviews

The reviews for Sage were fairly direct, with almost all reviewers praising how genius it feels to use automation instead of doing everything manually. So while we wanted to share reviews that discuss the unique features of Sage for eCommerce store owners, we simply couldn’t find any.

“I have 700 orders in Shopify that need to get entered into Sage 50 so rather than spending the next 3 months doing data entry, it will now all be done within a couple of days. Going forward this will be a daily task of about 5 minutes versus 2 hours which frees up our time to build our business.”

Windy Point Soap Making Supplies on


Comparison shopping based on price alone is a gamble. But when factored in with our other three points, it makes both dollars and sense.

Pricing for shopify accounting software

Here are considerations for the Shopify user:

  • We wanted to see that a free trial was available. This is a must, as accounting software can be a big investment.
  • Accounting software for your Shopify store should have the most necessary features available out-of-the-box, as in you shouldn’t have to immediately pay for an upgrade to get the basic functionality.
  • Your accountant should be able to login without too much hassle or having to pay for hidden fees of their own.
  • To be considered, there must be integration for Shopify, because this is such an immediate bookkeeping cost-savings.

You can take these prices below with a grain of salt, knowing that there could be promo codes or deals available with a little searching. Also, many of these software programs and integrations offer free trials.

Be sure to let your bookkeeper know that you’ll be signing up for integration, as this will greatly reduce their workload. If you have them manually pull in all of your Shopify data instead of using an integration, it will almost certainly cost you more money and introduce more errors, no matter how fast and accurate they are.

Quickbooks for Shopify Pricing

The ‘Plus’ plan costs $30 per month with the all-important ability to track inventory, and Quickbooks – Shopify Integrations start at $19.99 per month.

QuickBooks for shopify accounting pricing

When the dust settles, you’ll be paying about $50 per month to get started at the level you need as a Shopify store owner. And really, $50 is a drop in the bucket when you consider the firepower behind this accounting software. Anyhow, we found it to be a tremendous value.

Xero for Shopify Pricing

Xero is very much a pay-as-you-grow model. Let’s say that you’re still in the “growing” phase (but hopefully with more than 20 bank transactions per month). This software will cost you $30 per month. But looking a little deeper, we knew that Shopify Users would probably need the “Projects” capability in order to manage inventory, bringing the cost up to $60 per month. Combined with the cost of the integration ($39.99), you’re looking at approximately $100 per month.

Xero Shopify Accounting Pricing

Sage 50 for Shopify Pricing

Sage’s pricing for what a Shopify owner needs puts us in the “Premium Accounting” tier, and starts at $72.14 per month.

We had high hopes for Sage 50 until we discovered that the cost for the Shopify Sage integration alone is prohibitively high. You probably wouldn’t believe us if we said it’s $199 a month, so see for yourself:

Sage 50 Shopify Accounting Pricing

Honorable Mention (Pricing): Wave

One of our runners-up, Wave, is a very tempting accounting solution since it’s basically free. Their aggressive advertising puts them head-to-head with Quickbooks based on price, but their lack of inventory accounting options mean that it’s a no-go for serious Shopify store owners.

Quickbooks vs Xero vs Sage

Shopify store owners deserve a comprehensive review of their accounting options. After combing through hundreds of reviews, wading through often confusing cost structures, scaling the peaks and valleys of performance, and overturning the stones of popularity, we have created what we believe to be a fair report card for your Shopify accounting options.

Best Shopify Accounting Software

And yes…

Quickbooks turned out to be the clear choice when it comes to the best accounting software for Shopify. Be careful though, there are several integration options available, and not all of them deliver the goods.

But Flowify has you covered when it comes to syncing the two. The Flowify app integrates Quickbooks and Shopify with ease and elegance to completely automate sales tracking, inventory, refunds, processing fees, bank deposits, and more. Not to mention you’ll have organized and up-to-date business financials.

Get started with Flowify today and see how a support team of accountants and bookkeepers can help you to better manage your Shopify store accounting.

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