Purpose The purpose of the study is to indicate a three-dimensional convective heat transfer properties evaluation of magnetohydrodynamics nanofluid flow, comprising motile oxytactic microorganisms and nanoparticles, passing through a rotating cone. Design/methodology/approach The imposed technique for solving the governing equations is the Runge–Kutta fifth-order method. The main point of this survey is to diagnosis the influence of diverse factors on velocity, temperature distributions and concentration profile. Furthermore, appending the magnetic field, thermal radiation and viscous dissipation in calculations; also, simultaneous involvement of heat absorption and excretion has been represented as novelties. Findings The results elucidate that by changing the Peclet number from 1 to 2, the dimensionless concentration of the microorganisms has been diminished by about 34.37%. In addition, variation of the magnetic parameter from 0 to 1 has been resulted in reducing the temperature distribution by about 3.11%. Originality/value Recently, attention has been absorbed to adding the motile microorganisms to nanofluid for enhancement of heat transfer and avoiding aggregation of particles. In this regard, the hydrothermal flow of microorganisms has been investigated in this study.