Clear! Thanks 
We do this integration for a lot of our customers so please email evan@thedirectprocessors.com for more info and Shopify customers testimonials
Feel free to reach out if you need another payment processor. We save our merchants thousands and thousands of dollars
Hi there,
Your frustration is completely understandable, and you’re not alone.
Shopify charges an additional fee (e.g., 2% on the Basic plan) when you use a third-party payment provider, because you’re not using their in-house system, Shopify Payments. This fee is added on top of whatever the third-party processor charges — which can indeed push your total cost per transaction to 3–5%, depending on your setup.
Unfortunately, this fee isn’t tied to any specific support or service provided by Shopify at the time of payment — it’s simply part of their pricing structure for using external gateways.
Shopify justifies this as part of the cost of maintaining their ecosystem, but for merchants in unsupported countries especially, this often feels unfair — and in many cases, pushes people to look for more cost-efficient platforms.
If you are considering other payment options with lower fees, but still paying third party fees, this pay-by-bank vs shopify payment methods comparison may be helpful.
Hope this helps clarify things a bit.
It’s OK to use your third party payment provider. AFTER, you’ve collected payment from your third party provider, go to Shopify and create a CUSTOM ORDER. In Shopify: Create Order + Add a CUSTOM Item (can be from your product line, but just retype the product name along with price etc. + Click add item. Then, click “COLLECT PAYMENT”, scroll down and “MARK AS PAID”. Marking the item as already paid AVOIDS Shopify from charging you a fee. You’ll still be able to see the items listed among your orders and you can still fulfill the orders through shipping. Hope this helps. If it doesn’t call Shopify. Their reps are usually very helpful.
Yes, this is bad business practice! Say something. For larger businesses, this is an added cost of using Shopify!
Hello, does this method still work as of today? I am doing a lot of reading about how/when Shopify charges their third party transaction fees and it sounds like they charge them based upon completion of checkout….not when an order is marked as paid.
In addition I’m trying to do a test order and once the authorize.net gateway authorizes the transaction I don’t see a way to mark that order as paid without capturing the transaction.
you mentioned you do this integration for Shopify customers, are you talking about the authorize.net manual capture integration? I’m trying to figure out if this still works today as what I’m reading is that they capture their 3rd party fee when checkout is complete, regardless of if the transaction was “captured”
from Shopify AI support
“You’re correct! For Shopify Payments, processing fees are only charged when payment is captured, not when it’s authorized. However, third-party transaction fees for using providers like Authorize.net are charged when you use the third-party payment provider to accept customer payments, regardless of capture timing.
So with Authorize.net: you’ll pay Shopify’s third-party transaction fees, plus Authorize.net’s own processing fees when you capture payments externally.”
Good morning,
We have merchants using authorize.net that avoid the fee by settling the transaction in authorize.net instead of Shopify.
If you’d like more info I could get you more info in the next few days
@partha06 ridiculous take, shopify is a business they are not required to provide extra infrastructure[1] for free.
You want to play in another companies sandbox you play by their rules.
Don’t like it then use another tool.
Because they can, and you pay it proves it’s justified.
Don’t like it then use another tool and talk with your wallet.
[1] on extra infrastructure
Even if a merchant uses a different process shopify STILL have to monitor and support that in material ways in some cases they can’t choose to even NOT deal with it because it’s a financial and legal responsibility they legally cannot choose to ignore.
The 2 percent fee is basically Shopify’s way of charging for using their checkout and infrastructure when the payment is processed outside their system. It has been part of their pricing model for years and it only goes away if Shopify Payments is available in your country.
The frustration is valid though. If Shopify Payments is not supported where you are, the fee feels like a penalty you cannot avoid. Most merchants in unsupported regions move to a platform that does not add extra charges on third party gateways.
to reduce the impact without migrating, the only practical method is to tighten your payment flow and avoid unnecessary authorization attempts. Otherwise the fee structure will stay the same unless Shopify changes policy.
@PaulNewton this is exactly what I did. I moved my 3 shops to a different platform that charges 0% transaction fees.
If you have resources , cost comparisons etc, on migrating to a better platform for this issue please share.
That’s the REAL type of stuff other merchants come in here looking for even if the don’t know they need or resent hearing about it:
Escape hatches.
As a bonus since your the OP you should be able to mark your own post as the Solution: by getting rid of shopify transaction fees by just getting rid of shopify.
Delicious, made my day.
you are paying charges still ? Which Country are you from ?
This is an extra fee that Shopify charges if you use a payment provider or gateway other than Shopify Payments on Shopify Checkout.
Fortunately, there are third-party checkout solutions that work independently from Shopify Checkout and therefore do not incur these additional Shopify fees, for example: Shopify Stripe Checkout.