Temperature control for fermentation is crucial as it directly affects microorganism growth, productivity, and metabolic activity. This work proposes a modified fractional order proportional‐integral‐derivative (FOPID‐DF) controller that incorporates the system model in the control loop configuration utilizing a differential filter for precise temperature control within a narrow operating range. PID, fractional order PID (FOPID), modified fractional order PID (MFOPID), and fractional order internal model control (IMC) controllers were also designed for comparative analysis. The simulation results demonstrated that the proposed FOPID‐DF controller outperforms the other designed controllers, shown by a 22.33% reduction in integral absolute error (IAE) and a 29.06% decrease in integral square error (ISE) compared to the FOPID controller and various other improved performance indicators. Parameter variation and noise analysis highlighted the ability of the controller to maintain stability and performance under changing conditions. The simulation outcomes suggested that the FOPID‐DF controller excels in temperature control, ensuring optimal microorganism growth and metabolic activity.