I am making a website where I receive a percent-based commission on purchases conducted on my platform, between merchant and customer. I am planning on charging the merchants the total commission fees monthly.
Additionally, I also charge a recurring, flat monthly fee.
I have done this using Stripe’s plugin. You can use the Bubble built Stripe plugin to do this very easily. If you need PayPal, I think you would have to use Braintree (owned by PayPal). But you would need to create the API calls yourself
I do not know about the Philippines specifically. You will need to search the forums and Google to find a payment processor with a good API. Braintree and WePay are the only ones I can think of at the moment. Maybe someone else has a better answer