Supply Chain Quality Management (SCQM) modeling is one of the main research avenues in both academic and practitioner fields. Therefore, a SCQM model using a Multi-Layer Fuzzy Cognitive Map (ML-FCM) is developed in this paper. The ML-FCM model developed in this work allows expanding and decomposing SCQM concepts by grouping them as Fuzzy Cognitive Maps (FCMs) in multi-layers. The model was applied in a three-echelon supply chain in the sector of personal care products. The model construction and its capacity to represent the studied problem are analyzed through density and strength metrics. The inference process results validated the initial selection of the concepts in every FCM and allowed to quantify the effect of each echelon on SCQM performance. The most important decision making variables for SCQM improvement in the studied supply chain were total profit, quality costs, suppliers rejections and returns, productivity, and customer rejections and returns .