Hi, I was facing this issue as well, so here is what I have figured out and I hope it will help whoever is still facing this issue as well.
Firstly, please go to this link (https://avada.io/shopify/docs/how-create-custom-manual-payment-method-shopify.html - disclaimer: I am not the creator of the site, so not receiving any benefits at all) and figure out how to create a custom manual payment method yourself, and from there you should see a field that says "Payment Instructions". This is a more crude way to go about achieving this, but, you will have to inform your customer to scan the qr code at the final page after pressing the pay now button. On your end, you will have to ensure that the payment is received before the order is being processed, sadly to say, I am still trying to figure out how to optimize this process.
Secondly, proceed to your shopify settings and click on checkout. Scroll down to the field that says "Additional Scripts" and paste this script within it:
<img src="insert image URL here" alt="QR Code">
For my own website, I used this code to add the QR code:
<img src="https://cdn.shopify.com/s/files/1/0269/2032/1126/files/qr_code.jpeg?v=1593514889" alt="Shopify QR Code">
Do note that the "insert image URL here" refers to the unique URL for your qr code. A simple way to go about obtaining that URL is as follows:
In your Shopify admin's "Settings" -> "Files" -> "Upload files" section which will auto generate a unique URL for the image. Once you have the image, you can use the image's URL and implement it in the code above.
I have attached are some of the images of the final product. I am just an amateur in this, pardon the crude way of doing things :) hope this helps, stay safe and blessed!