The protocol for analysis of rock-forming mineral compositions by X-ray electron probe microanalysis used at the Institute of Geology and Mineralogy, Novosibirsk, Russia, is described. The analysis is conducted with a JXA-8100 electron probe microanalyzer capable to support a highly stable beam at relatively high probe currents for a long time. Elements that can be assayed range from sodium (atomic number Z = 11) to zinc (Z = 30). The operation conditions for routine analyses are substantiated: accelerating voltage 20 kV, probe current 50–100 nA, and signal accumulation time 10 s at both the peak and the background. The method of analytical problem formulation for measurements is presented. It is proven that the proprietary software is insufficient with the presence of the binary matrix effect and better correction methods are required. Metrological characteristics of the protocol have been studied. The variation coefficient, describing the reproducibility of results, averages 0.9% for major components (C > 10%), 2.5% for minor components (1 < C < 10%), and 6.8% for accessory components (0.3 < C < 1%). With still lower contents (0.05 < C < 0.3 %), the standard deviation of reproducibility is 0.02%. The values of the variation coefficient and standard deviation for measurement repeatability are approximately two times lower. The relative trueness of the method is within 1%. The detection limit (3σ criterion) is generally within 0.01–0.03%. It can be improved by an order of magnitude by increasing the accumulation time and probe current.