We have a portal where merchants can fetch their orders from Shopify and our app is fully free but our portal has subscriptions we have implemented PayPal when the merchant opts for any subscription. But Shopify App Review Team rejected it all time, So where do I have to implement this Billing API?
Make your App non-free. When a merchant installs your App, they will be challenged to accept your App. At this time, you are free to decide how to bill them to use your App. If your portal charges money externally to merchants, to access Shopify, you need to instead move that charge to inside your App. So you stop charging via Paypal and your Portal, and instead, charge the same fee inside your App. When a merchant goes to install your App, and you recognize they have no subscription, that is where you redirect to code in your App to create a subscription. Shopify will give you an URL to redirect to, and then the merchant can decide to accept your subscription.
That is how you get your App accepted.
Custom Shopify Apps built just for you!