This paper presents a MILP-based decomposition algorithm for solving large-scale scheduling problems with assembly operations in flexible flow shop environments. First, a rigorous mixed-integer linear (MILP) formulation based on the general precedence notion is developed for the problem under study. Then, the MILP model is embedded within a decomposition algorithm in order to accelerate the resolution of large-size industrial problems. The proposed solution approach is tested on several examples derived from a real-world case study arising in a shipbuilding company.