Selection of appropriate welding parameters in micro-friction stir welding (micro-FSW) is challenging and a practical problem. In this regard, an assessment of variation in the favourable process parameters due to downscaling of sheet thickness can prove beneficial. In this work, FSW in 1- and 0.5-mm-thick AA6061-T6 sheets was compared for suitable process parameters based on the tensile strength of the weld. Comparatively high tool rotational speed combined with a high speed of tool travel and low plunge depth was found to be suitable welding parameters in micro-FSW (0.5-mm sheet). The effect of using this favourable set of process parameter was also assessed on frictional heat input requirement per unit weld volume, deformation conditions during welding (predicted using FEM simulation) and weld’s mechanical properties and microstructural characteristics in each sheet thickness. A high frictional heat input per unit weld volume was found in micro-FSW. A reduced weld zone temperature, an increased value of strain rate and a higher cooling rate were found in micro-FSW which led to a smaller weld nugget grain size, an improvement in weld’s ultimate tensile strength (UTS) but a drop in its ductility in this case.