The potential for climate change and temperature shifts to affect ecosystem stability remains relatively unknown. One mechanism by which temperature may affect stability is by altering trophic interactions. The functional response quantifies the per capita resource consumption by the consumer as a function of resource abundance and is a suitable framework for the description of nonlinear trophic interactions. We studied the effect of temperature on a ciliate predator-prey pair (Spathidium sp. and Dexiostoma campylum) by estimating warming effects on the functional response and on the associated conversion efficiency of the predator. We recorded prey and predator dynamics over 24 hours and at three temperature levels (15, 20 and 25 degrees C). To these data we fitted a population dynamic model including the predator functional response, such that the functional response parameters (space clearance rate, handling time, and density dependence of space clearance rate) were estimated for each temperature separately. To evaluate the ecological significance of temperature effects on the functional response parameters we simulated predator-prey population dynamics. Effects of increased temperature included a transition of the functional response from a Type III to a Type II and an increase of the conversion efficiency of the predator. Stability analysis via simulation showed destabilisation of the system likely caused by a transition from Type III to a Type II, with greater risk of prey extinction at higher temperature. Warming-induced shifts from a Type III to II are not commonly considered in modelling studies that investigate how population dynamics respond to warming. Future studies should investigate the mechanism and generality of the effect we observed and simulate temperature effects in complex food webs including shifts in the type of the functional response as well as consider the possibility of a temperature dependent conversion efficiency.