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Mineral processing deals with complex particle systems with two-, three- and more phases. The modeling and understanding of these systems are a challenge for research groups and a need for the industrial sector. This Special Issue aims to present new advances, methodologies, applications, and case studies of computer-aided analysis applied to multiphase systems in mineral processing. This includes aspects such as modeling, design, operation, optimization, uncertainty analysis, among other topics. The special issue contains a review article and eleven articles that cover different methodologies of modeling, design, optimization, and analysis in problems of adsorption, leaching, flotation, and magnetic separation, among others. Consequently, the topics covered are of interest to readers from academia and industry.