A focused ion beam (FIB) system coupled to a scanning electron microscope, including a new helium-cooled stage and electrical feedthroughs, has been put into operation. It allows real-time electron imaging during FIB machining while the sample is maintained at a minimum temperature of 25 K by continuous-flow helium cooling. Simultaneously, electrical characteristics can be monitored, recorded, and stored. Experimental results on high-critical-temperature superconducting thin films are given, exhibiting the evolution of the device’s response during the FIB-induced modifications. Two structures were realized at liquid-nitrogen temperature : a low-noise microbolometric sensor and a short-channel superconducting quantum interference device-like structure in YBaCuO material exhibiting a behavior of coherent vortex flow, micromachined by FIB. These experiments demonstrate the possibility of a precise in situ control of the critical current of micro- and nanobridges.