DocumentationConfiguring feesWhat the percentage is based on
What the percentage is based on
A percentage needs something to be a percentage of. Out of the box that is the cart subtotal plus the cart's tax, because the Taxes box starts ticked. Three other boxes add shipping and other fees, or take coupons away.
The default
The base starts at the cart subtotal, excluding tax and before shipping. With every box unticked, a 2 % fee on a basket of $100 in goods is $2.00, whatever shipping and tax come to.
One box starts ticked, though: Taxes. So a fee set up fresh takes its percentage from the subtotal plus the cart’s tax — 2 % of $121, not of $100, on the basket below.
The four options
Each checkbox adds something to the base before the percentage is applied, and they combine — so tick them and watch. Same 2 % fee, $100 subtotal, $10 shipping, a $20 coupon, $21 tax on the goods, and a $5 gift-wrap fee another plugin put on the order:
One basket
- Goods$100
- Shipping$10
- Coupon− $20
- Tax on the goods$21
- Gift-wrap fee, from another plugin$5
Include in the percentage calculation
The percentage is taken from$100 + $21$121
so a % fee comes to$2.42
This is how a fee starts: Taxes ticked and nothing else, so out of the box the percentage includes the cart’s tax.
Fees means fee lines other plugins added — a gift-wrap fee, a handling fee. This plugin’s own fee is never in its own base.
One caveat about that box: at checkout WooCommerce has not totalled any fees yet at the moment this plugin calculates, so ticking it adds nothing there. It only has an effect on the orders Pro writes a fee onto afterwards — the order-pay page and admin-created orders.

Combined
They stack. Shipping and Coupons together feed subtotal + shipping − coupon
into the percentage: $100 + $10 − $20 = $90, 2 % = $1.80. Shipping and
Taxes together add the shipping tax as well as the goods tax.
The rule of thumb: tick whatever your payment provider charges you a percentage of. A card processor charges on the whole amount the customer pays, so tick shipping and taxes. A cash-on-delivery courier charges on the cash it collects, which comes to the same thing.
Coming from 2.x
The defaults are version 2’s: Taxes is on, the other three off, so a fee set up fresh in 3.0 charges what the same numbers charged in 2.x. An upgraded store keeps whatever it had ticked.
The rest of the arithmetic — caps, tax, rounding — is on how the amount is calculated.
Need the base to be something none of the four give you — one product's price, say? A filter does it; the reference names it.
Filter reference