Modern methods of in situ transmission electron microscopy (TEM) allow one to not only manipulate with a nanoscale object at the nanometer-range precision but also to get deep insights into its physical and chemical statuses. Dedicated TEM holders combining the capabilities of a conventional high-resolution TEM instrument and atomic force -, and/or scanning tunneling microscopy probes become the powerful tools in nanomaterials analysis. This progress report highlights the past, present and future of these exciting methods based on the extensive authors endeavors over the last five years. The objects of interest are diverse. They include carbon, boron nitride and other inorganic one- and two-dimensional nanoscale materials, e.g., nanotubes, nanowires and nanosheets. The key point of all experiments discussed is that the mechanical and electrical transport data are acquired on an individual nanostructure level under ultimately high spatial, temporal and energy resolution achievable in TEM, and thus can directly be linked to morphological, structural and chemical peculiarities of a given nanomaterial.