This work focuses on the study of bioconvection in a conical region of rotating and stationary cone-disk systems utilizing nanofluids involving gyrotactic micro-organisms. The flow geometry encompasses two different configurations, namely, rotating cone-disk system (RCDS) and stationary cone-disk system (SCDS). For RCDS, four unique configurations are considered: rotating cone static disk (Model-I), static cone rotating disk (Model-II), co-rotating cone-disk (Model-III), and counter-rotating cone-disk (Model-IV), while SCDS includes both swirling and non-swirling flow scenarios. A total of six different physical configurations that differ in boundary conditions are investigated. The mathematical model comprises Navier–Stokes, energy, nanoparticle volume fraction (NVF), and micro-organism density equations. The novelty of the work lies in the development of a Lie-group self-similar model to describe the physical phenomenon, which is compatible with that of literature in the absence of gyrotactic micro-organisms. How the different flow configurations contribute to the flow and heat transport features is studied in detail. Among four RCDS configurations, the rotating cone static disk exhibits the maximum heat transport at the disk surface. Notably, the effects of micro-organism density ratio and bioconvection Peclet number demonstrate consistency across all configurations, offering comprehensive insights into these complex fluid systems. The findings highlight the critical role of flow type in nanofluid applications and emphasize the necessity for meticulous consideration in system design and optimization. This research contributes valuable insights to the field of bioconvective nanofluid dynamics in cone-disk systems, with potential implications in conical diffusers, medical devices, and viscosimeters.