Present research is aimed to analyze the performance factors of flexible manufacturing systems by combined decision-making methodologies like analytical hierarchy process (AHP), combinatorial mathematics-based approach (CMBA) and improved ELECTRE. Six variables affecting the three factors of performance of flexible manufacturing systems viz. productivity, flexibility and quality are considered for the evaluation of performance factors. The weights of the attributes are calculated with AHP and the index score is calculated with CMBA methodology. CMBA methodology is the fusion of AHP and GTMA. ELECTRE approach has been used for the outranking of factors. The results show that productivity had the maximum impact on the performance of manufacturing systems. A high Spearman’s rank correlation also exists among the methods used.