You can batch multiple transactions from a single customer together to avoid paying the Stripe fee on each charge. To do this, you first need to save the customer’s payment information. Then you can either:
Bundle the payments locally and create a charge automatically through your own system,
Subscribe your customer to a $0/month plan and create an invoice item for each small payment. By default, Stripe will pay the invoice automatically with each billing cycle.
Alternatively, you can create the invoice immediately and pay it.