Design and synthesis of batch plants must consider scheduling aspect simultaneously. In this paper, MINLP problems arising in very general flexible batch plants design and synthesis are solved by a stochastic MINLP optimiser. The formulations considered include linear/nonlinear models for capital cost processing units/storage vessels and processing task models with fixed, linear and nonlinear processing time in a general form. The MINLP optimiser, based on an Evolutionary Algorithm with Simulated Annealing does not require convexity and smoothness of the problem formulation, and a suitable original encoding procedure is reported. Several examples are given to demonstrate the method’s efficiency and the quality of the solution.