Variable flux permanent magnet synchronous machines (VF-PMSMs) use permanent magnet magnetization as an additional degree-of-freedom to reduce losses based on operating conditions (e.g., at medium to high speeds, losses are reduced by using a lower magnetization). Magnet properties are known to be dependent on temperature; therefore, the magnet temperature effects on magnetization manipulation and maximum torque properties in VF-PMSMs are investigated in this paper with FEA simulations and experiments. Increased magnet temperature changes the available range of attainable magnetization levels and makes demagnetization occur more easily; therefore, a different current angle and magnetization are needed for maximum torque operation. The temperature effects on high speed magnetization manipulation methods, which are needed for driving cycle loss reduction and full power capability, are evaluated with simulation and experiments on a prototype 80 kW traction machine. A closed loop method for magnetization manipulation that mitigates the effect of temperature is proposed.