Semiconductor nanowires have demonstrated fascinating properties with application in a wide range of fields including energy and information technologies. In particular, increasing attention has been focused on Si and SiGe nanowires for application in thermoelectric generation after recent successful implementation in miniaturized devices. Despite this interest, an appropriate evaluation of thermal conductivity in such nanostructures still poses a great challenge, especially if the characterization of the device-integrated nanowire is desired. In this work, a spatially resolved technique based on scanning thermal microscopy has been demonstrated for the assessment of the thermal conductivity of Si and SiGe nanowires integrated in thermoelectrical microgenerators. Thermal conductivity values of 15.8 ± 0.8 W m-1 K-1 and 4.2 ± 0.3 W m-1 K-1 were measured for Si and SiGe nanowires, respectively, epitaxially grown on silicon microstructures. Moreover, the range of applicability according to the sample thermal conductance and associated errors are discussed to establish the potential of the novel technique. The results presented here show the remarkable utility of scanning thermal microscopy for the challenging thermal characterization of integrated nanostructures and the development of multiple devices such as thermoelectric generators or photovoltaic cells.