AbstractThis study investigates heat, mass transport, and entropy production in Ellis nanofluid flow through an inclined permeable microchannel, considering Navier's slip effects with convective boundary conditions. It incorporates nanoparticle's thermophoresis and Brownian motion effects under a transverse magnetic field, with fluid suction and injection at microchannel walls. Under appropriate physical assumptions, the problem is presented as nonlinear ordinary differential equations, which are later nondimensionalized. The MATLAB bvp4c solver is used for numerical solutions of the transformed equations. Graphical depictions in the study illustrate how various factors influence velocity, temperature, concentration, Bejan number, and entropy generation. Engineering parameters, affected by changes in critical factors, are presented in tabular format, including the skin friction coefficient, Nusselt number, and Sherwood number. Notably, the enhancement in Ellis fluid parameter has a dual effect, enhancing velocity and Bejan number in the microchannel's lower half, while reversing in the upper half. For the increment in Ellis parameter, the impact on Bejan number for 0.5 is significant and the effect on entropy production contrasts with that of Bejan number. This research offers practical insights for designing efficient microfluidic heat exchangers and developing advanced nanofluids for improved thermal performance while minimizing entropy generation. Additionally, it underscores the potential for innovation within the domain of microfluidics and nanomaterial‐driven heat transfer systems. Furthermore, it should be noted that the flow behavior of Ellis nanofluids within microchannels can closely replicate natural flow patterns found in biological systems, offering insights that could have numerous applications in biology and related fields.