Electron backscatter diffraction (EBSD) generally links crystallographic orientation to the microstructure of crystalline materials. EBSD datasets are now commonly used to identify phases, grains, and their orientations using off-the-shelf software, although substantial additional information may be extracted. Due to the lack of commercially available software, advanced analyses are often done manually and provide only localised information, lacking statistical significance. Here we introduce novel automated methodologies for advanced analyses of microstructural features in Ni-based superalloys. Our methodologies provide additional insights into the characteristics of these features and their underlying physical phenomena. We showcase how to correct wrongly indexed γ/γ’ interface artefacts in combined EBSD and energy-dispersive X-ray spectroscopy (EDS) measurements, how to classify recrystallised grains based on their location, how to assess and visualise grain boundary planes, and how to study the evolution of Σ3 twins during hot deformation. We further demonstrate how phase fractions and grain sizes are more accurately determined in combined EBSD-EDS measurements. The classification of recrystallised grains into different groups enables individual analyses, facilitating the straightforward identification of the underlying recrystallisation mechanism. Our grain boundary plane analysis provides insights into the coherence of Σ3 twins and the potential boundary planes of incoherent Σ3 boundaries. The current paper is a tutorial-style guide for these methodologies. The algorithms are made freely available and, although demonstrated here on Ni-based superalloys, can also be applied to other systems.