Spin crossover (SCO) molecules are promising nanoscale magnetic switches due to their ability to modify their spin state under several stimuli. However, SCO systems face several bottlenecks when downscaling into nanoscale spintronic devices: their instability at the nanoscale, their insulating character and the lack of control when positioning nanocrystals in nanodevices. Here we show the encapsulation of robust Fe-based SCO molecules within the 1D cavities of single-walled carbon nanotubes (SWCNT). We find that the SCO mechanism endures encapsulation and positioning of individual heterostructures in nanoscale transistors. The SCO switch in the guest molecules triggers a large conductance bistability through the host SWCNT. Moreover, the SCO transition shifts to higher temperatures and displays hysteresis cycles, and thus memory effect, not present in crystalline samples. Our results demonstrate how encapsulation in SWCNTs provides the backbone for the readout and positioning of SCO molecules into nanodevices, and can also help to tune their magnetic properties at the nanoscale.