This study explores the optimization of Casson fluids, focusing on the role of ternary hybrid nanofluids in enhancing thermal efficiency in industrial and engineering applications. Specifically, the impact of thermophoretic particles and chemical reactions on bioconvective Casson ternary hybrid nanofluid flow through a vertical microchannel embedded with porous media is examined. The governing equations are reduced using similarity transformations, and the resulting nonlinear equations are solved using the Runge–Kutta–Fehlberg 4th and 5th order method. The findings reveal that increasing the thermophoretic constraint leads to a decrease in nanoparticle concentration, highlighting the impact of thermophoretic forces on particle movement and deposition. Additionally, the porous parameter causes a reduction in flow velocity, which is observed to affect the overall fluid dynamics in the system. The presence of variable thermal conductivity enhances the thermal field, suggesting that temperature distribution can be significantly improved. Moreover, increasing the nanoparticle volume fraction enhances temperature distribution, indicating a positive correlation between nanoparticle concentration and thermal efficiency. On the other hand, increasing the thermophoretic constraint results in a decrease in mass transfer rate, emphasizing the trade-off between enhanced thermal performance and reduced mass transport. These findings are valuable for the design of advanced micro-cooling devices, micro-heat exchangers, micro-pumps, and macro mixing technologies, where both thermal and mass transfer performance are critical.