Optimise Peltier cooling system: PWM or not?
Using PWM without smoothing causes increased I2R losses in the Peltier element that reduces the available cooling and efficiency.
Ideally you need to run the Peltier element with DC that is proportionally controlled to the level needed to maintain the cooling.
The controller can use high-speed PWM with inductive filtering to increase overall electrical efficiency.
This app note from TI is relevant and shows actual measurements comparing PWM drive with constant current drive. In their example the constant current achieved about 8° better cooling and nearly 40% more efficient: Driving a Peltier Element