The product quality of a fermentation process depends on a number of factors such as temperature, pH, nutrient balance, dilution rate, dissolved oxygen and CO2 concentration etc. The present work focuses on the precise temperature control of the process and to achieve desired product quality. Therefore a novel control algorithm, which is an amalgamation of fractional mathematics and IMC-PID, having less design parameters is proposed. A fractional order IMC-PID is designed and then modified (MFOIMC-PID) by incorporating an extra control loop with proportional gain to reduce the offset error. A nature inspired optimization technique i.e. water cycle algorithm is utilized for estimation of optimum design parameters of proposed controller which leads to WMFOIMC-PID controller. Fractional order PID (FOND) and conventional PID are also designed for comparative study. Simulation results show that the proposed controller reduces integral absolute error (IAE) by 57% and 72% in comparison to FOPID and PID respectively for set-point tracking. Similar reduction of IAE is observed for disturbance rejection and noise suppression. Thus WMFOIMC-PID proves to be more robust and efficient in comparison to the other designed controllers. (C) 2017 Institution of Chemical Engineers. Published by Elsevier B.V. All rights reserved.