A normal subscription charges once per delivery. A prepaid one separates the two: the customer pays for a whole period upfront and still receives the deliveries one by one. Three months paid today, one box a month for three months.
Expand the delivery option and set Delivery frequency to how often the customer receives something, for example 1 month. Prepaid billing is built on top of that number, so get it right first.

Open More: free shipping, custom name, prepaid under the frequency and discount, then tick Prepaid subscription. A note appears saying "Customer pays upfront for the entire billing period and receives deliveries at the frequency set above", followed by two fields.
Enter a number under Billing frequency and pick the unit under Billing interval. For monthly deliveries paid a quarter at a time, that is 3 and months.
The billing period has to be longer than the delivery period. If it is not, saving stops with "Billing period must be longer than delivery period for prepaid subscriptions". Near-equal periods are refused too: 5-week deliveries with monthly billing.
The collapsed option gets a badge reading "Prepaid, billed every 3 months", and the widget preview shows the same wording as a chip on that option. The plan name starts from the delivery rhythm and the billing period is added after it. The app punctuates that name with a dash, so at checkout it reads "Deliver every month, Prepaid — Billed every 3 months".
A prepaid option is paid by card, not by iDEAL or Bancontact. Shopify only offers a payment method it can charge again later, and the local methods create a single payment, so a prepaid cart skips the "Pay with iDEAL" button and goes straight to the normal checkout. Nothing is mispriced and nobody is overcharged: the shopper simply pays the whole prepaid amount by card. Your pay-per-delivery options keep the iDEAL button exactly as before.
This means a store that takes only local payment methods, with no card gateway at all, cannot sell a prepaid option. The plan editor says so and keeps the setting switched off there, so you never build a plan nobody can buy.
If most of your customers pay with iDEAL or Bancontact, you can offer the same deal without the prepaid setting: sell a bigger package, delivered less often. A 3-month supply delivered every 3 months costs the customer the same as three monthly deliveries paid upfront, but technically it is an ordinary subscription: one payment per delivery. That works with every payment method, needs no special handling, and the customer sees one clear price.
To set it up, create a product variant sized for the longer period (for example "90 capsules" next to "30 capsules"), then give it a delivery option matching that period, with its own discount if paying for more at once should cost less. The one real difference from prepaid: the customer receives everything in one parcel instead of a delivery each month. For supplements, coffee or pet food that is usually fine, and you save on shipping too.
Keep a normal pay-per-delivery option in the same plan, so customers who do not want to pay upfront still have a choice.
Give the prepaid option its own discount, since paying upfront is worth a better rate.
Stuck on any of this? Open the chat in the bottom right corner of the app and we will help you set it up.