Many of the novel 2D superconducting films with highly crystalline structure and atomic thickness, fabricated in ultrahigh vacuum chambers, are highly vulnerable to air exposure, making it difficult to measure intrinsic superconducting properties such as zero resistance and perfect diamagnetism with ex situ experimental techniques. To realize vacuum-based measurements, we developed a multifunctional scanning tunneling microscope. The conventional STM probe in the microscope can be switched, under vacuum conditions, to a two-coil probe that can detect whether a material exclude magnetic flux. By using this in situ mutual inductance technique, for the first time, we succeeded in detecting the intrinsic diamagnetic response in both two-atomic-layer indium film on a Si(111) surface and monolayer FeSe films on SrTiO₃. The Si(111)-√7 × √3-In films is expected as a conventional superconductor according to previous STM study. Our diamagnetic measurements verify that the low-temperature variation of penetration depth in Si(111)-√7 × √3-In films follows the BCS theory in the dirty limit. On the other hand, the behavior of monolayer FeSe films on SrTiO₃ in the external magnetic field indicates a vortex melting picture.