The efficiency of kesterite-based solar cells is limited by various non-ideal recombination paths, amongst others by a high density of defect states and by the presence of binary or ternary secondary phases within the absorber layer. Pronounced compositional variations and secondary phase segregation are indeed typical features of non-stoichiometric kesterite materials. Certainly kesterite-based thin film solar cells with an off-stoichiometric absorber layer composition, especially Cu-poor/Zn-rich, achieved the highest efficiencies, but deviations from the stoichiometric composition lead to the formation of intrinsic point defects (vacancies, anti-sites, and interstitials) in the kesterite-type material. In addition, a non-stoichiometric composition is usually associated with the formation of an undesirable side phase (secondary phases). Thus the correlation between off-stoichiometry and intrinsic point defects as well as the identification and quantification of secondary phases and compositional fluctuations in non-stoichiometric kesterite materials is of great importance for the understanding and rational design of solar cell devices. This paper summarizes the latest achievements in the investigation of identification and quantification of intrinsic point defects, compositional fluctuations, and secondary phases in non-stoichiometric kesterite-type materials.