The only real difference is fulfillment
On the same listing, Amazon's referral (commission) fee is the same whether you run FBA or FBM. What actually changes your margin is how the order is fulfilled: under FBA you pay a per-unit fulfillment fee plus monthly storage; under FBM you pay your own shipping and packaging. This tool isolates exactly that trade-off.
When FBM wins — and when FBA does
FBM tends to win per unit for large, heavy or slow-moving items where FBA fees and storage are high and your own shipping is cheaper. FBA tends to win for small, fast-moving items — and it brings faster delivery, the Prime badge and a Buybox edge that can lift volume enough to beat a slightly higher FBM unit margin. Compare the per-unit numbers here, then weigh the volume effect.
Know your floor either way
Whichever model you choose, don't discount below the point where the sale stops being profitable. Find that price with the minimum sale price calculator, and see the full deduction stack with the Amazon profit calculator and Amazon FBA calculator.
Method and sources
Net = sale price − referral fee (rate × the total the buyer pays, plus 20% VAT) − (FBA fee + storage, or your shipping) − product cost. Sales VAT is treated as pass-through. Enter the current FBA fee for your product's size/weight from Seller Central; fees and storage change over time and must be verified there.