Afterpay fees

Shopify Discussion
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Topic summary

Merchants are frustrated with the combined 8% fee structure for offering Afterpay: 6% charged by Afterpay plus an additional 2% from Shopify for using third-party payment providers.

Key concerns raised:

  • Small businesses with 10-15% profit margins find these fees unsustainable, especially when competing with larger corporations that reportedly pay around 3% to Afterpay
  • One merchant contacted Afterpay requesting fee reduction but was denied, with Afterpay stating they cannot negotiate merchant fees
  • Additional frustrations include fees calculated on total order amount (including shipping), rolling reserves of 30% held for 3 months on new businesses, and inability to pass fees onto customers

Disputed details:

  • Some confusion exists about whether the 2% Shopify fee is truly additional or absorbed by Afterpay, with one user claiming it’s charged monthly with store subscription
  • The fee structure reportedly includes both percentage and fixed transaction fees

Potential workarounds mentioned:

  • Exploring alternative third-party payment providers
  • Using Shopify Stripe Checkout or “Easy⇼Pie Shopify Stripe Checkout” to avoid the extra 2% fee
  • Switching to Klarna, which was integrated into Shopify Payments and no longer carries the additional charge

Many merchants are considering removing Afterpay entirely due to unsustainable costs.

Summarized with AI on October 24. AI used: claude-sonnet-4-5-20250929.
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I contacted afterpay to see if they can help reduce fees, the 6% they charge plus the recent addition of 2% shopify adds on top made me have to remove it as payment method see below:

My email: (edited to remove any personal or Shopify account details)

hope this email finds you well. I am reaching out regarding the reintegration of Afterpay to my Shopify store

Previously, I had to remove Afterpay from my store due to Shopify implementing an additional 2% fee to

use your service, which brought the total fee per transaction to 8% (6% to Afterpay + 2% to Shopify).

As a small business owner, maintaining profitability is crucial. With an average profit margin of 10-15%

per sale, the current payment fees significantly impact my ability to sustain operations.

After deducting 8% in payment fees, there is minimal profit left to reinvest in the business.

I understand that larger corporations like Ali** enjoy lower transaction fees, approximately 3%.

In order to continue utilizing Afterpay on my Shopify store and remain profitable, I kindly request a

reduction in fees to a level similar to what Ali*** and other major corporations pay. Reducing thee Fees to 3% would make it feasible for me to continue offering Afterpay as a payment option to my

customers while ensuring the sustainability of my business.

I appreciate your attention to this matter and look forward to your response.

Their reply:

Hi

Just following up on the fee reduction query as well.

Unfortunately at this stage we can’t negotiate your merchant fees.

We understand this probably isn’t the news you were hoping for. However, while we can’t

(renegotiate/refund) your fees, we’re doing everything we can to provide you with the support we know

you need, including continuing to market and connect your business with our loyal customer base, and

importantly, continuing to partner with you to offer customers a responsible way to spend.

It’s important to remember that Afterpay is not a bank or a traditional credit product – we are the

opposite.

We only charge you when a sale is successfully processed – we don’t charge any standing per

terminal, store, or month fees.

We guarantee your payment while assuming all customer risk for you (customer fraud or

chargebacks).

We pay your business upfront – well before the end of the customer repayment cycle – and in

doing so help improve your cash flow.

We use this scale and reach to deliver on our main priorities – providing value to you, our retail partners,

and linking your businesses with customers across the globe.

We’re confident that our business model will hold us and our partners in good stead now and into the

future.

My reply:

Yes I used afterpay for my business before and I am already set up with integration but I had to remove

it as a payment method because Shopify started adding 2% extra to fee bringing it to 8% in total. As a

business trying to compete with amazon where Chinese FBA sellers are bypassing tax obligations to

compete with local businesses we need to keep margins low to be competitive and pay tax as well as

import fees etc, this leaves almost nothing left and add to this afterpay that NOW even Ali****

offers, it’s not possible. I can’t understand how this is even fair to my business trying to do everything

right and I can’t even offer afterpay to my customers anymore if I want to make a profit…

hopefully if enough people complain

either Shopify or your team will do something to bring fees to a amount more manageable 8% is not fair and reasonable at all!

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Hi @aaron111111 !

Upon checking, Afterpay is part of the Third-party providers and Shopify does have 2% third party transaction fees as this are an external payment processor. If Afterpay have additional 6% transaction fees on their end, I now it is not ideal though, it would be best to keep an open communication with them regarding this and workarounds. They can also further explain regarding these fees.

As a workaround, I suggest that you explore other third-party payment providers that Shopify supported in your location to see what works or the best fit to your current business.

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their fees are insane. You also have to remember the 8% also includes any shipping which may be based off a real time calculator. So the 8% is even more for some products if basing it off the product margin. It’s actually criminal for small businesses. Then they allow massive corporations to have very low Afterpay fees.

Also, they lie when they say the risk is all theirs. They always keep 30% of the order amount for 3 months on new businesses. They most definitely invest this combined rolling reserve and make astronomical amounts of money off it. If you receive even a single chargeback they will go back to holding 30% of your money and THEY WILL use that money if chargebacks occur. that’s 30% of money that IS NOT THEIRS. It is like if you went to a restaraunt and paid them with visa and someone from VISA took 30% of that restaraunts transaction and just invested it for 3 months…

But you know shopify don’t care. They hate small businesses. They could so easily add a fee surcharge option where we could charge customers the full 6% to use Afterpay but they never will. Check out threads on this. Shopify never respond or they say they are passing it onto the “improvements team”. They side with Afterpay. they know Afterpay would hit back so hard if shopify dared to allow us to pass on Afterpay’s criminal surchage to customers.

This isn’t just Afterpay. It is all BNPL. also it isnt 8%, it’s 8% + the fixed fee per transaction.

All BNPL is criminal and shopify not providing an easy solution for small business to pass on that fee and deter customers from using the criminal BNPL services shows all you need to know about what shopify thinks of small businesses.

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Well said!

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I’ve researched this and the 2% fee for using a third party payment method is absorbed by AfterPay, the 2% fee is not seen in order transactions, and it’s not incorporated into the settlement amount that comes from AfterPay. If you have a 6% AfterPay Fee, that’s the total fee you lose on the total transaction amount, so you don’t need to add 2% + 6%.

(From what I can tell, I could be wrong but if I am then Shopify is doing something super suss by not logging deductions anywhere in the admin).

I don’t see that they’ve deducted it from upcoming payouts either, again I could be wrong but if I am then they are being proper suss with how they aren’t disclosing it.

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the 2% fee shopify takes is charged monthly with your store subscription, they add up very fast

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Just saw this post as I am thinking very seriously about dropping afterpay. Its ridiculous. I listen to ppl all the time say oh AP is great…we pay no interest. I said no you don’t but the businesses get charged heaving for offering it. And I only just found out that shopify was charging 2% on top of that (plus apparently a fixed fee as well). OMG as a small business that just rips in to your small profit. Plus we can’t pass AP fees on to the customer for using the service as according to AP that is discrimentary against customers that choose to pay that way. Yeh think for my business its not worth offering it anymore and losing those customers.

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Don’t have much to add here apart from I stumbled upon this when considering adding Afterpay as an option. It is indeed 6% + 2%.

A couple of things:-

Shopify want to push their own BNPL product (Shop Pay) so no doubt they won’t be in a rush to remove that 2%.

I will say though that Klarna used to have this additional charge and is now administered within Shopify Payments (additional third party % was dropped) so there could be some light at the end of the tunnel if you’re still using Afterpay.

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Shopify Stripe Checkout is available with no additional commissions, only Stripe fees listed on the Stripe pricing page. It supports most of the payment methods supported by your Stripe account, such as Klarna, Afterpay and more.

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Check out “Easy⇼Pie Shopify Stripe Checkout”, with this solution, you won’t have Shopify’s extra 2% fee.

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