<p>This study investigates heat transfer and entropy generation in the flow of a Prandtl-Eyring fluid in a porous microchannel, motivated by the need to optimize micro scale thermal and fluidic systems for energy, biomedical, and environmental applications. Understanding how non-Newtonian fluid behaviour interacts with variable thermal conductivity, heat sources, and pollutant transport is critical for designing efficient and sustainable microfluidic devices. The governing partial differential equations are transformed into ordinary differential equations using dimensionless variables and solved numerically via fourth-fifth order Runge-Kutta-Fehlberg method combined with the shooting technique. The results show that entropy generation decreases with increasing thermal conductivity and material parameters, but increases with the heat source parameter. A dual behaviour is observed for the slip parameter, where entropy generation trends differ near the channel walls compared to the channel central portion. The concentration of the fluid raises with both external and local pollutant sources, highlighting the system’s sensitivity to pollutant inflow. For motile microorganisms, the concentration increases with the bio-convection Lewis number due to intensified thermal gradients, but decreases with the bio-convection Peclet number as stronger advection causes dilution. A dual behaviour in the irreversibility ratio is also noted for varying heat source parameter. Furthermore, the heat transfer rate is enhanced by increasing the heat source parameter, while drag force decreases with higher material parameter values. These findings provide insights into the thermo fluidic behaviour of non-Newtonian flow in porous micro-channels and have practical relevance for energy systems, biomedical devices, and microfluidic technologies. Applications include drug delivery, pollutant control, and thermal management in compact electronic or biological systems, where precise control of heat, mass, and entropy generation is essential.</p>