Many atomically thin exfoliated two-dimensional (2D) materials degrade when exposed to ambient conditions. They can be protected and investigated by means of transport and optical measurements if they are encapsulated between chemically inert single layers in the controlled atmosphere of a glovebox. Here, we demonstrate that the same encapsulation procedure is also compatible with scanning tunneling microscopy (STM) and spectroscopy (STS). To this end, we report a systematic STM/STS investigation of a model system consisting of an exfoliated 2H-NbSe2 crystal capped with a protective 2HMoS2 monolayer. We observe different electronic coupling between MoS2 and NbSe2 from a strong coupling when their lattices are aligned within a few degrees to essentially no coupling for 30° misaligned layers. We show that STM always probes intrinsic NbSe2 properties such as the superconducting gap and charge density wave at low temperature when setting the tunneling bias inside the MoS2 band gap, irrespective of the relative angle between the NbSe2 and MoS2 lattices. This study demonstrates that encapsulation is fully compatible with STM/STS investigations of 2D materials.