Power crisis, global warming and various environmental issues have constantly emphasized researchers to discover sustainable and environmental-friendly alternative energy resources. Bio-electrochemical systems, significantly microbial fuel cells (MFCs) can harvest bioenergy from organic wastes and treat them simultaneously. Flow parameter investigation has been conducted in innovative flow straightener implemented honey comb MFCs (HCMFCs) in the current research study. The impacts of flow channel diameter on the performance of the HCMFCs operated in recirculation batch mode have been estimated in the current study. Three different diameters like 0.4 cm, 0.7 cm and 1 cm are used in three reactors as HCMFC1, HCMFC 2 and HCMFC 3 respectively along with a control reactor devoid of flow straighteners. Numerical simulation models are presented for reactor performance portrayal. The power performance is analyzed by Nyquist plots, polarization curves, power density curves and equivalent circuits. Result justification is accomplished by anode biofilm thickness analysis using scanning electron microscope. HCMFC 2 showcased the best performance by achieving a voltage generation of 0.55 V, current density of 5300 mA/m2, power density of 430 mW/m2, organic content removal of 97.6%, reduced internal resistance and with the thickest anode biofilm. These innovative reactors will effectively enhance research and provide great prospects for future applications.