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Shopify Payments Review: The Pros And Cons Of Shopify’s Integrated Payment Processor

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Liz Hull

Liz Hull

Liz Hull is a writer for Merchant Maverick. In her three years with Merchant Maverick, she has tested and reviewed over 40 eCommerce platforms and published two ebooks on the topic of online selling. Liz has also been published in Startup Nation and Home Business Magazine Online. Liz has a BA in English and Spanish from George Fox University.
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Responses are not provided or commissioned by the vendor or bank advertiser. Responses have not been reviewed, approved or otherwise endorsed by the vendor or bank advertiser. It is not the vendor or bank advertiser's responsibility to ensure all posts and/or questions are answered.

    Christy Stocker

    I recently switched from Etsy to Shopify, and Shopify decided that because I’ve gotten a bunch of orders in a short period of time, I’m “under review” with my payment account frozen. I got a notice Sept 20 that I needed to provide proof of address (utility bills in my name – I don’t have any, they’re in my husband’s name), business & tax licenses, front and back of driver’s license, proof of tracking/shipping receipts for ten packages, and business social media links (my shopify acct is connected to my FB and IG accounts, so this info should already be available to them). The letter said I would have a week to upload required docs, or my payment account might be put on hold. ONE MINUTE LATER, I got a second email saying my account was on hold. I’ve been in touch with them, to explain about the utility bills, remind them I’ve already sent pics of mail to my address from the state gov’t, and my ID with proof of address. I’ve heard nothing back – no apology for shutting my account down, no confirmation that it will ever be opened up again. Tomorrow will be a week that my account has been frozen for no good reason.

      Nathan Calvert

      I’ve identified some major problems with international eCommerce using Shopify Payments. As we have a UK bank account but with Euro, USD and AUD accounting facilities, Shopify Payments only allows payout in GBP (based on our physical location), so we’re losing 2-3% on every transaction to conversion fees (which completely negates the transaction fee discounts the platform offers). On top of this, the majority of our customers are being charged a foreign transaction fee (3%) by their banks (regardless if currency is like for like). It all appears to revolve around Shopify’s single currency pay out policy, if we had the ability to receive pay outs in multiple currencies (such as WorldPay, Ogone, Braintree and Paypal all allow) it would solve this problem, and allow us to use localised holding accounts. I would love to keep Shopify Payments for all of it’s benefits (faster checkout, ePos, Wholesale channels and cross platform integration is unparalleled, plus it’s surprisingly good with B2B and tax exemption control) – but given its limitations for international eCommerce I can’t see any other option here but to find alternatives.


        I’m considering whether to use Shopify or not to start an ecom store. I’ve just watched a webinar from a shopping cart platform that is offering a lifetime account with zero transaction fees. One still must pay the payment processor fees (Stripe, PayPal, etc) but not the per-transaction fee that Shopify and many other shopping cart platforms charges. This platform (which I won’t name because I am not an affiliate) claims to integrate with Shopify. I’m curious to know if Shopify will even allow someone to use a 3rd party cart to get around their per-transaction fee?

          Jessica Dinsmore

          Hi Don,

          We’ve never heard of integrating another shopping cart with Shopify to avoid transaction fees. However, there are lots of shopping carts out there that do not charge transaction fees. We like BigCommerce and 3dcart. Both of them are affordable, user friendly, and neither charges transaction fees.


            I’ve seen some stores that are in the “high risk” category which shouldn’t be eligible for Shopify Payments, but they are using it anyway. Is that because they haven’t been caught yet or is there some room for exceptions/negotiation?

              Jessica Dinsmore

              Hi Lauren,

              It is very likely that these high risk merchants have not yet been caught by Shopify Payments. Payment service providers (PSPs) like Shopify Payments and Stripe (which operates Shopify Payments) often initially accept merchants and allow them to begin processing without actually reviewing their account. Then, some weeks or months later, the PSP does an official review of the business using their service. It is at that point that they may deem a business “high risk” and revoke their payment services.

              Shopify Payments’ Terms of Service states:

              “We may terminate this Agreement and close your Service Account at any time for any reason effective upon providing you notice in accordance with Section A16 above. We may suspend your Service Account and your access to the Service and any funds in your Service Account, or terminate this Agreement, if (i) we determine in our sole discretion that you are ineligible for the Service because of the risk associated with your Service Account, including without limitation significant credit or fraud risk, or for any other reason; or (ii) you do not comply with any of the provisions of this Agreement, (iii) upon request of an Organization or the a card issuer.”

              We’ve included more information on Shopify Payments and businesses that qualify/don’t qualify for services in the article we are commenting on as well.

                Liz Brown

                They could be using a different gateway than Shopify Payments. Shopify itself lets you sell things that you can’t process through Payments, due to the limitations Stripe places, instead of Shopify itself.

                There are gateways all over the world that are integrated with Shopify, so it could be one of those that they have on their stores.

                  Eric Chang

                  I have been looking for this answer for a while.

                  I have a customer who made a $1.5k purchase and wants a refund. He is returning the item but unfortunately I already spent the payout to pay my manufacturers and there is only $200 in pending payout balance.

                  Does Shopify credit your refund first? or can the customer not receive the refund until I have money in the bank or pendint balance?

                    Jessica Dinsmore

                    Hi Eric,

                    We found this answer in the Shopify Help Center. It only applies if the seller processed the payment through Shopify Payments:

                    “If you are using Shopify Payments and you issue a refund, then the amount is deducted from your next available payout. A refund usually takes 3 to 5 business days to be credited back to your customer. If you are in the United Kingdom, Ireland, Singapore, New Zealand, or Spain and your payout doesn’t have enough funds for the refund, then the remainder of the refund is deducted from the next payout until the refunded amount is covered. For other regions using Shopify Payments, if your payout doesn’t have enough funds, then the balance is debited from your bank account on the day of the payout.
                    If a negative balance payout fails, then the payout will try again in 3 business days. For more information about issuing refunds with Shopify Payments, see the Shopify Payments FAQ.”


                      My question is about the merchant fees. We currently use Authorize as a third party payment option and on the top of the standard payment processing fees, we are also charged merchant fees from all the credit cards we captured payments from (VISA, MC, AMEX and ect) which run between 2%-4%. So when shopify has a pricing of 2.9% plus 0.30 per transaction, is this all we would be paying related to all credit card transactions or that is just shopify’s cut and we pay the additional merchant fees?

                        Rose Holman

                        Hello, thanks for your question. Shopify Payments uses a flat pricing model, so 2.9% + $0.30 transaction fee covers all your wholesale fees from the card networks, plus Shopify Payment’s cut. You of course also must pay a monthly subscription fee to Shopify for using the software (starting $29/month for a full online store).

                        Hope that helps answer your question. If you need more information on how processing fees work with different pricing models, check out: our complete guide to rates and fees.

                          Saroni Kundu

                          Since Braintree is a Paypal company now, does Shopify intergrate with Braintree? Also what is the transaction feel that Shopify will charge on top of Braintree fee charge?

                            Rose Holman

                            Braintree is not available as a processor with Shopify. Their partnership ended in 2016, so only current Braintree + Shopify users could continue using Braintree as a processor from that point (no new accounts).


                              I have 2 separate businesses one that is service based and one that is product based. Can I use Shopify Payments for the products and use stripe to connect with my other software of service so payments are in one place?

                                Rose Holman

                                Hi, Deanne. I’m not 100% sure I’m understanding your question properly, but I’ll take a stab at it. Shopify Payments, while built on Stripe’s payments infrastructure, is not the same as Stripe on its own. As far as I know, a Stripe dashboard and a Shopify Payments dashboard for managing payments won’t be integrated or accessed in the same place — especially if you’re using Shopify software for your physical products and integrating Stripe with different software for your service business. In the sense that payments will both ultimately pass through Stripe-based systems as some point, they’ll be in the “same place,” but that’s about it.

                                The bottom line: you can definitely use both processors at the same time, that shouldn’t be a problem — but your interaction with your transactions and reporting may not be quite as “all in one place” as you’re envisioning. It’s best to think of Shopify Payments as a separate payment gateway.

                                Hope that helps, let us know if we’ve misunderstood what you were asking!

                                  Valerie Trainer

                                  If I integrate my store from Etsy, how does Shopify get paid. Will they automatically take their money from my sales like Etsy has started to do, or will I have a payment that is due once a month? As a small business a lot of sellers on Etsy feel betrayed by their last move to do this!!!! Please explain because I’m sur a lot of sellers on Etsy would like to know!! Thank you for TRANSPARENCY!!!

                                    This comment refers to an earlier version of this post and may be outdated.

                                    Rose Holman

                                    Hi, Valerie. There’s a couple components to this depending on your situation.

                                    If you use Shopify Payments as your payment processor, a card processing fee of 2.9% + $0.30 (or less if you’re on a higher Shopify subscription plan) will be taken out of each sale in real time, and you will receive the net sales amount in your account. You will also be billed your monthly subscription to Shopify, of course.

                                    If you do not use Shopify Payments and choose an alternate gateway instead, Shopify will also charge an extra commission per sale on top of your card processing fee, which will also be taken out in real time. This fee ranges from 0.5% to 2% depending on which Shopify subscription plan you have. Meanwhile, you will be charged separately for card processing fees from your chosen alternative gateway (you’ve got over 100 options to choose from for alternative gateways to use with Shopify.). These card processing fees will also mostly likely be taken out automatically in real time.

                                    The reason it’s done this way is that they don’t want you to be able to withdraw funds before fees are taken out, so the fees have to be taken out as the transactions come in.

                                    It’s kind of confusing, so I hope that helps answers your question!

                                      This comment refers to an earlier version of this post and may be outdated.


                                      Question…..can i use my Square mobile app to manually process payments from customers? Would I just send an invoice to the customer myself?

                                        This comment refers to an earlier version of this post and may be outdated.

                                        Jessica Dinsmore

                                        Hi Diggy,

                                        You can send an invoice directly from within Square, but Shopify Payments also has the same ability and costs exactly the same. As far as we know, Shopify and Square don’t integrate directly, so you’d need a third-party tool that would cost more money. Shopify does integrate with PayPal and you can use PayPal alongside Shopify Payments without incurring additional transaction fees. That would also allow invoicing. But again, it’s the exact same cost.

                                        I would recommend that you first check out Shopify Payments’ invoicing tools and decide whether you like them as much as Square’s invoice tools, and go from there.

                                          This comment refers to an earlier version of this post and may be outdated.


                                          Hello, I am a little bit confused about Shopify payment, that’s why i have a few questions.
                                          If I use basic Shopify payment (monthly price 29$) shopify charges me 2.9%+30c per transaction. is that right? But if I use Shopify payemnt+ an external gateway such as paypal, does it mean I should pay for per transaction 2.9%+30c + 2%(for transaction fee) or it only charges me 2% as transaction fee?

                                            This comment refers to an earlier version of this post and may be outdated.

                                            Liz Hull

                                            Hi Anahit,

                                            I’m happy to clear things up!

                                            Shopify Payments works as your payment gateway for your Shopify online store, so you won’t need to add another gateway on top of it. However, you may choose to do so. If you choose to list multiple gateways, you may need to pay Shopify’s transaction fee. Here are your options below (assuming that you’re accepting payments for an online store rather than in-person):

                                            Basic Shopify Plan ($29/month) + Shopify Payments (2.9% + $0.30 credit card rate) – NO Transaction Fee
                                            Basic Shopify Plan ($29/month) + External Gateway (gateway’s credit card rate, likely around 2.9% + $0.30) + Shopify’s Transaction Fee (2%)

                                            If you choose to combine Shopify Payments with an external gateway in order to give customers more payment options, you will have to pay that 2% Shopify transaction fee on any payment that goes through your external gateway. You will never have to pay the transaction fee on payments that go through Shopify Payments.

                                            There is one exception to this rule, and that is PayPal. Shopify has negotiated with PayPal to offer you a deal on using Shopify Payments and PayPal together. If you choose to use Shopify Payments and add on PayPal, you will not have to pay that 2% Shopify transaction fee on any payments. Keep in mind that you will still be paying the 2.9% + $0.30 credit card rates on all your Shopify payments transactions, and PayPal credit card rates on all your PayPal transactions.

                                            Hope that helps!


                                              This comment refers to an earlier version of this post and may be outdated.


                                              I have just been advised I cannot use shopify payments as I have been deemed high risk, does this mean if I accept PayPal, I will be charged the additional 2% on toof PayPal fees?

                                                This comment refers to an earlier version of this post and may be outdated.

                                                Liz Hull

                                                Hi Darren,

                                                That is correct. You will have to pay the additional transaction fee on top of PayPal Fees. That fee is 2% on Shopify’s Basic Plan. Higher plans have lower transaction fees (1% on the Shopify Plan and 0.5% on the Advanced Shopify Plan), but if you don’t/can’t use Shopify Payments, you will always have that fee.


                                                  This comment refers to an earlier version of this post and may be outdated.


                                                  Their pay period so short, that’s good news for sellers. i may start selling sooner on shopify.

                                                  Thanks for your good post.

                                                    This comment refers to an earlier version of this post and may be outdated.


                                                    Hello! A quick question. If one builds an ecommerce site with Shopify+Shopify Payments, who is the merchant of record?

                                                      This comment refers to an earlier version of this post and may be outdated.

                                                      Jessica Dinsmore

                                                      Hi Emanuel,

                                                      Great question! Shopify Payments is powered by Stripe, and as a third party processor we suspect the merchant of record would be Stripe, but we can’t say for sure. What we do know, is that the merchant in this scenario, would not be listed as the merchant of record.

                                                        This comment refers to an earlier version of this post and may be outdated.

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                                                      Our unbiased reviews and content are supported in part by affiliate partnerships, and we adhere to strict guidelines to preserve editorial integrity. The editorial content on this page is not provided by any of the companies mentioned and has not been reviewed, approved or otherwise endorsed by any of these entities. Opinions expressed here are author’s alone.