Nowadays, manufacturing systems are much larger with an increasing number of production lines and units. As a result, the decision-making of manufacturing system is a non-trivial problem and requires complex control subsystems. The use of Programmable Logic Controllers (PLCs) allows to program various and non-standard solutions. In the paper the application of Multi-Attribute Decision-Making (MADM) methods to a decision-making related to flow control in a manufacturing system with three production lines is described. For this purpose, the SAW (Simple Additive Method), WASPAS (Weighted Aggregated Sum Product ASsessment) and TOPSIS (Technique for Order Preference by Similarity to Ideal Solution) methods are applied and simulated with using manufacturing system model in Matlab Simulink and SimEvents. In methods subjective weights defined by an expert are used. However, in order to move away from subjectivism, Shannon’s entropy is used for determining weights of criteria. The used approaches have been compared.