A fryer includes a fryer pot, a filter pan connected to the fryer pot by a drain conduit and a return conduit forming a filtration loop, a cooking oil quality sensor being in the filtration loop, and a controller that controls operation of a filtration cycle of the fryer. The filtration cycle has a circulation sequence and a fill sequence. The circulation sequence circulates cooking oil through the filtration loop and the fill sequence fills the fryer pot with the cooking oil from the filter pan. The controller stops the fill sequence after filling the fryer pot with a predetermined amount of cooking oil during a partial fill and resumes the fill sequence after a predetermined amount time elapses to complete the fill sequence. The cooking oil quality sensor measures a cooking oil quality to obtain a cooking oil quality measurement during the predetermined amount time.
