Micro/nanoscale fabricated devices have widely been used in modern technology and bioengineering as they offer excellent heat transfer. Removal of excess heat, coolant selection, rapid mixing, and handling proportion of colloidal metallic nanogranules in the base fluid are the main challenges in micro/nanofluidic systems. To address these problems, the primary motivation of the intended mathematical flow problem is to investigate the thermal and flow aspects of blood-based ternary nanofluid in the presence of inclined magnetic field and thermal radiations through a microfluidic pump with elastic walls. Further, the pump inner surface is smeared with fabricated cilia. The embedded cilia blow in coordination to start metachronal travelling waves along the pump wall that assist homogenous mixing and manipulation. The entire analysis is conducted in moving frame and simplified under lubrication and Rosseland approximations. Numerical solution of various flow and thermal entities are computed via the shooting method and plotted for different values of the parameters of interest. A comparative glimpse allows us to conclude that the trimetallic blood-based nanofluid exhibits elevated heat transfer rate by 12–18%, bi-metallic by about 11–12%, and mono nanofluid by about 6% compared to the conventional blood model. The study also determines that the prolonged cilia commence augmentation in flowrate and pressure-gradient around the pump deep portion. Furthermore, the radiated ternary liquid under fragile magnetic field effects may contribute to the cooling process by eliminating unnecessary heat from the system. It is also noticed that around the ciliated wall, the heat transfer irreversibility effects are appreciable over the fluid frictional irreversibility.