This study investigates the entropy generation optimization for synthetic cilia regulated ternary hybrid Jeffery nanofluid (Ag–Au–TiO₂/PVA) flow through a peristaltic vertical channel with swimming motile gyrotactic microorganisms. The research explores the interaction of multiple physical phenomena in biomedical applications, focusing on the effects of electroosmotic MHD, Joule heating, viscous dissipation, thermophoresis, Brownian motion, thermal radiation, and chemical reactions. The governing partial differential equations are transformed into ordinary differential equations using appropriate transformations and solved numerically with the shooting technique using BVP5C in MATLAB. The velocity, temperature, concentration, electroosmosis, and microorganism density profiles are analyzed for different emerging parameters. The study also presents graphical investigations of engineering interest quantities such as heat transfer rate, mass transfer rate, skin friction coefficient, and entropy generation optimization. The results show that the rate of mass transfer increases with the thermophoretic parameter, while the reverse effect is noted for the Brownian motion parameter, Schmidt number, and chemical reaction number. The study highlights the importance of understanding the intricate interactions of multiple physical phenomena in optimizing entropy generation and advancing microfluidic systems. The findings have potential applications in studying cilia properties of the respiratory tract, reproductive system, and brain ventricles. The research introduces a novel paradigm by synergizing electroosmotic MHD effects, ternary hybrid Jeffery nanofluids, and gyrotactic microorganisms in ciliated vertical channels, offering new insights into energy efficiency and bio transport understanding. The study also discusses the thermophysical properties of the ternary hybrid nanofluid and the mathematical expressions for the governing equations. The results are validated against existing studies, and the numerical solutions are presented for the boundary value problem using the shooting method. The study provides a comprehensive analysis of the effects of various parameters on the flow characteristics, heat transfer, mass transfer, and entropy generation in the system.This study investigates the entropy generation optimization for synthetic cilia regulated ternary hybrid Jeffery nanofluid (Ag–Au–TiO₂/PVA) flow through a peristaltic vertical channel with swimming motile gyrotactic microorganisms. The research explores the interaction of multiple physical phenomena in biomedical applications, focusing on the effects of electroosmotic MHD, Joule heating, viscous dissipation, thermophoresis, Brownian motion, thermal radiation, and chemical reactions. The governing partial differential equations are transformed into ordinary differential equations using appropriate transformations and solved numerically with the shooting technique using BVP5C in MATLAB. The velocity, temperature, concentration, electroosmosis, and microorganism density profiles are analyzed for different emerging parameters. The study also presents graphical investigations of engineering interest quantities such as heat transfer rate, mass transfer rate, skin friction coefficient, and entropy generation optimization. The results show that the rate of mass transfer increases with the thermophoretic parameter, while the reverse effect is noted for the Brownian motion parameter, Schmidt number, and chemical reaction number. The study highlights the importance of understanding the intricate interactions of multiple physical phenomena in optimizing entropy generation and advancing microfluidic systems. The findings have potential applications in studying cilia properties of the respiratory tract, reproductive system, and brain ventricles. The research introduces a novel paradigm by synergizing electroosmotic MHD effects, ternary hybrid Jeffery nanofluids, and gyrotactic microorganisms in ciliated vertical channels, offering new insights into energy efficiency and bio transport understanding. The study also discusses the thermophysical properties of the ternary hybrid nanofluid and the mathematical expressions for the governing equations. The results are validated against existing studies, and the numerical solutions are presented for the boundary value problem using the shooting method. The study provides a comprehensive analysis of the effects of various parameters on the flow characteristics, heat transfer, mass transfer, and entropy generation in the system.