PayPal was acquired by eBay in its early days in 2002, and the two firms have worked in partnership ever since.
The changes mean that while eBay buyers can still pay with PayPal, sellers will be paid straight into their bank accounts.
But some sellers have threatened to stop using the service over the move.
EBay's forums have several posts from sellers who say they are reluctant to use the new system and give eBay direct debit access to their personal bank accounts.
But the new terms, effective from 1 June, say the new "managed payments" system is compulsory, and the company has the power to limit or remove listings from sellers who refuse to use it.
The company says the new system is simpler, convenient, and gives buyers more payment options - and the rollout will be gradual.
It marks a significant change in an almost two-decade partnership with PayPal, which split from eBay in 2015.