The MakerDAO Stability Fee is calculated against the Dai drawn on your CDP
You can think of the Stability Fee as the interest rate you pay for minting (i.e., borrowing) Dai. The Stability Fee accrues continuously and can be paid in either MKR or Dai. MKR token holders determine the Stability Fee percentage through Maker’s governance system, known as the MakerDAO. Composed of MKR token holders, the MakerDAO maintains and secures the Maker credit system by voting on issues that affect the system’s growth and stability. Thus, MKR holders are in charge of ensuring that the Dai supply fits the market’s demand for Dai.