For sample preparation prior to mineral analysis, microwave digestion (~2 h) is quicker and requires lower acid volume as compared to dry (6–8 h) and wet digestion (4–5 h). However, microwave digestion had not yet been compared systematically with dry and wet digestion for different cheese matrices. In this work, the three digestion methods were compared for measuring major (Ca, K, Mg, Na and P) and trace minerals (Cu, Fe, Mn and Zn) in cheese samples using inductively coupled plasma optical emission spectrometry (ICP-OES). The study involved nine different cheese samples with moisture content varying from 32 to 81% and a standard reference material (skim milk powder). For the standard reference material, the relative standard deviation was lowest for microwave digestion (0.2–3.7%) followed by dry (0.2–6.7%) and wet digestion (0.4–7.6%). Overall, for major minerals in cheese, strong correlation was observed between the microwave and the dry and wet digestion methods (R2= 0.971–0.999), and Bland–Altman plots showed best method agreement (lowest bias), indicating the comparability of all three digestion methods. A lower correlation coefficient, higher limits of agreement and higher bias of minor minerals indicate possibilities of measurement error.