Hey @Rahul_Chopra,
Take a look at Payment Customization Functions. These are Shopify Functions that let you hide, reorder, or rename payment methods directly at the platform level without touching CSS. You can create logic that detects when a customer was redirected from your mobile app (using cart attributes, customer tags, or other identifiers) and then hide the “Pay on Delivery” option for those specific cases.
Check out the payment customization tutorial to get started. The example shows how to hide payment methods based on conditions.
You could also use checkout blocks for this as well. Shopify Checkout Blocks - Checkout Blocks | Shopify App Store