I found contradicting answers from Shopify forum whether COD transaction will be charged. The explanation in this page https://help.shopify.com/en/manual/your-account/manage-billing/your-invoice/charges is unclear too.
My questions: will I be charged on COD transaction if I don't use Shopify Payment? And whether the answer is the same if the COD transaction is created via API rather than Shopify Secure Checkout?
This is Max from the Shopify Team.
Short answer, no. Manual payments (aka payment captured outside of the Shopify checkout, where you arrange to receive their payment outside your online checkout) are no longer subjected to transaction fees. Cash on delivery is one way that you could capture a manual payment.
I've added some more details below, just in case you, or anyone else reading this might need some further details.
This is from the doc on transaction fees you mentioned:
If you don't use Shopify Payments or a manual payment method, then transaction fees apply on orders brokered by Shopify in addition to the credit card rate charged by your payment provider.
It is more explicitly stated in the doc on manual payments:
You won't be charged transaction fees for manual payments.
If you ever have questions about your invoice or any other questions about selling with us, feel free to reach out to support directly. Let us know if this answer was helpful, or if you need some more details!