How to proceed with billing API for a free ERP SaaS Shopify App?

Shopify Apps
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Hi,

We run a ERP SaaS application for breweries and we use a Shopify App to copy orders from Shopify back into our software for reposrting and logistics. We charge for our SaaS application but we do not charge for using the Shopify App.

I am currenctly in a review process for an unlisted app, and have been told numerous times that we must use the Shopify Billing API - and as we charge for the SaaS application the app cannot be free.

We have a deep integrated billing system, and cannot use Shopify Billing API for our charges (we also integrate with many other ecommerce platforms and most of our customers do not use Shopify - therefore it really does not make sense to use it).

I’m stuck at the moment as partner support keep directing me to billing support, and billing support just keep saying use the billing API but offering no clarity for our use case. The last message stated that i should use a $0 one off payment but that seems a bit silly, plus is different to what i have added to the pricing details on the app listing.

Has anyone been in this situation and figured out a way to proceed?

Thanks.

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Hello @fango256

We just went through the approval process for Glass It Price Tracker, a price tracking solution that can boost your profit margins while staying competitive in your target market. We also had several existing integrations with other platforms prior to developing our Shopify App. I will only share our experience, as the Shopify requirements can change.

You must implement the Shopify Billing API to be a public app listed in the Shopify App store with any sort of billing charges. Shopify Partners only make exceptions in a few cases, most of which seem related to billing for physical products provided/consumed outside of the Shopify App. In our case, because of our existing integrations we had to identify when a user signs up using our Shopify App. In these instances we always use the Shopify Billing API for any billing charges for those users. The Shopify Billing API applies whether or not the user who signs up using the Shopify App actually uses the Shopify App, or instead uses our website or mobile app for any billing charges. In short, there is no way around using the Shopify Billing API for users/leads who became customers sourced from the Shopify App store, unless you qualify for an exemption from the Billing API. Hope this helps!

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Comforting that it is not just us they are picking on. Frustratingly we are
applying to be unlisted, so will get no traffic from the app store. Yet
apparently this requirement remains! Thank you for taking the time to
respond.

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Hey @fango256 - wondering on how you progressed with this? anything helpful you can share? we are similar situation and would like to learn how to work this out.
thanks for sharing!

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Hey @fango256 , we’re in the same boat as you. We have a SaaS application, which includes access to a free Shopify app for those who have Shopify stores. The app is one tiny piece of our service.

We’re being forced to move our private app (installed across lots of stores) to a public app – otherwise the app’s API access will be revoked. We’re happy having the app unlisted since we just want our customers to be able to install it.

Shopify wants their cut, and requires use of the Billing API. I’m curious how you resolved your situation, if you’re willing to share.

Thanks!

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Same here, we are building a Shopify app as a bridge between Shopify and our larger IT platform. Our products also have a large operational component, not just SaaS (i.e., purely software). The app is a nice-to-have that would be offered to a subset of clients to facilitate their integration with us. It’s a minimal part of the entire product offering.

I might be misreading this entire conversation? Would Shopify expect us to bill the entire invoice (for all our services) to clients if they use our Shopify app? Even if the app is unlisted and Shopify contributes nothing to us being discovered by clients?

Has anyone else figured out a resolution to this issue?

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I’m afraid i have no good news to share for our use case. This was a wildly frustrating experience, we reached out to ambassadors and Shopify employees directly and got nowhere. Which has led to me having a pretty strong dislike to Shopify as a developer platform.

Anyway that aside, we started looking at our competitors and other smaller companies such as ourselves and noticed that many just guided users to make custom apps on their site and plug the keys back into their own platform. Despite being against T&Cs.

I told Shopify that was what we noticed and they just parroted the documentation back to me and decided not to comment.

Make of that what you will.

1 Like
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hi @fango256 - we’re also a SaaS company going through the app review process. similar to what you experienced, we weren’t able to get around the billing API requirement, so we’re in the process of developing a solution.

curious if you ended up publishing to the app store? would love to understand what your approach was for the billing API if you’d be willing to share. Shopify doesn’t seem to have many requirements around how the Billing API gets implemented, what’s most important to them is that it gets implemented some way or another.

thanks!

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Exactly right Shopify just wants the Billing API implemented for anyone who signs up from Shopify. If you can figure that out you’re good and should get approved on the Shopify App Store.

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we’re in about the same boat. we don’t necessarily even need the shopify data for our platform to work.

curious about what solution you’re developing. Bc shopify isn’t essential to our app I’m hesitant to do anything that labor intensive

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Unfortunately we ended up having to build out a custom billing solution through Shopify. We created three annual plans for net-new customers who discover us on the app store and want to procure our services directly through Shopify. Since Shopify is only facilitating the billing and not the contracting process, we also worked with our legal team to create new T&Cs for those that procure our services through Shopify. There are some special terms we had include in our T&Cs as Shopify lets merchants downgrade or cancel a subscription for an apps services by simply selecting a lower plan or uninstalling the app.

For our existing customers, we built an option for them to bypass the billing flow as long as they have login credentials to our platform.

This has been a ton of work, and given the segment of the market we cater to (primarily enterprise brands) it doesnt really make sense for us to bill through Shopify, but the Billing API was hard requirement to get our app listed so we decided to make the investment as we have so many customers re-platforming to Shopify right now.

With Shopify’s move up-market, I sure do hope they make some changes around how they onboard and certify app partners who are in the enterprise ecosystem.

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Our Experience with the Apliiq Print On Demand Shopify App & Shopify Billing API

Hi everyone,

I’d like to share our experience with the Apliiq Print On Demand Shopify App, particularly regarding the recent transition to the Shopify Billing API.

Our app enables merchants to print and brand premium apparel products, with fulfillment handled directly to their customers. We initially launched as a custom app in 2016 and installed it in over 500 stores. However, due to Shopify’s 500-store limit for custom apps, we were required to transition to a public app in 2018. At that time, Shopify explicitly allowed us to bill merchants directly since we were manufacturing and shipping physical products—something we confirmed in writing.

Fast forward to 2025, and Shopify has now mandated that we transition to the Shopify Billing API. Despite providing our previous written approval, Shopify rescinded its prior commitment and informed us that failure to comply would result in the de-listing of our app. We were given a two-week deadline to implement the new billing system.

While we have an experienced in-house development team proficient in Shopify’s API and payment processing, this sudden and unplanned change was a significant distraction. However, we adapted and completed the integration. Unfortunately, we discovered several critical challenges with the Shopify Billing API that were not clearly communicated by Shopify. While Shopify emphasizes the benefits of the system, there are some notable drawbacks that merchants and developers should be aware of:

1) Payment Delays

The Shopify Billing API introduces significant delays in payments. Unlike credit card transactions that clear within hours or checks that process within a week, Shopify Billing can take months to remit payments. Even with active subscriptions and confirmed charges, we have yet to receive payments that should have been processed weeks ago. Although Shopify publishes a payment schedule, in our experience, they do not consistently adhere to it.

2) Risk of Non-Payment

Unlike traditional payment processing, where a successful charge ensures you receive funds, Shopify Billing does not guarantee payment. If Shopify is unable to collect funds from the merchant, you will not get paid—even if the system initially confirms the transaction, even though merchants have been enjoying the benefits of your app. This is not comparable to a credit card chargeback; rather, it means that if a merchant’s payment fails when Shopify attempts to collect, the partner (you) simply does not receive the expected revenue. There is no recourse or alternative solution.

3) Lack of Transparency & Reporting Challenges

Accessing a report of activated subscriptions is unnecessarily complex, requiring multiple steps through the partner dashboard. Once located, the subscription list lacks sufficient detail, making it difficult to reconcile payments with internal systems. Additionally, there is no straightforward way to track unpaid or missing payments. If you contact Shopify Partner Support for assistance on a specific missing payment, they will be unable to provide merchant-specific details unless you are a collaborator on the merchant’s account, instead directing you to reach out to the merchant yourself.

4) Higher Costs & Administrative Burden

Shopify states that they take 15% of app revenue, but they also charge a 2.9% processing fee through Shopify Payments. In reality, this equates to a 17.9% total deduction. This is a relatively high processing fee & revenue share, especially considering you have to offer benefits without guarantee of payment. Reconciling these charges directly from Shopify adds an additional layer of complexity for developers managing financial records and for accounts that need to reconcile accounts and statements.

Final Thoughts

Overall, the forced transition to Shopify Billing API, the lack of support, and the system’s inability to efficiently perform its core function—billing and collecting payments—have made this process frustrating. While we’ve adapted to these changes, the experience has been less than ideal.

For those who have implemented Shopify Billing API, what has your experience been like? Have you encountered similar challenges, or have you found any effective workarounds?

Looking forward to hearing your thoughts.

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About 1 month into billing, with Shopify api, I wanted to provide a quick udpate. Of the 40+ subscriptions, we haven’t received payment for 2 of them (both 4 weeks old). Basically a 5% nonpayment rate [email removed] 4 weeks.

Is anyone else auditing their payments from the billing api, and have you seen a non payment rate this high?

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Very informative articles. Keep it up.

“SaaS for Business Success” This is one of the more informative articles must read everybody.