Improving the performance of manufacturing systems is a vital issue in today’s rival market. For this purpose, during the last decade, scientists have considered more than one objective function while scheduling a production line. This paper develops a 4-phased fuzzy framework to identify effective factors, determine their weights on multi-objective functions, and, accordingly, schedule manufacturing systems in a fuzzy environment. The aim is to optimize product completion time and operational and product defect costs in a job-shop-based multi-objective fuzzy scheduling problem. In the first and second phases of the proposed framework, it was shown that the existing uncertainty of the internal factors for the studied cases causes the weights of factors to change up to 44.5%. Then, a fuzzy-weighted NSGA-II is proposed (FW-NSGA-II) to address the developed Non-linear Fuzzy Multi-objective Dual resource-constrained scheduling problem. Comparing the outcomes of the proposed method with other solving algorithms, such as the Sine Cosine Algorithm, Simulated Annealing, Tabu Search, and TLBO heuristic, using seven series of comprehensive computational experiments, indicates the superiority of the proposed framework in scheduling manufacturing systems. The outcomes indicated that using the proposed method for the studied cases saved up to 5% in the objective function for small-scale, 11.2% for medium-scale, and 3.8% for large-scale manufacturing systems. The outcomes of this study can help production planning managers to provide more realistic schedules by considering fuzzy factors in their manufacturing systems. Further investigating the proposed method for dynamic product conditions is another direction for future research.