A novel methodology is presented in this work to minimize the manufacturing objectives, namely tolerance cost and machining time for allocating optimum tolerance to the components of complex assemblies with considering the proper process and machine selections from the given alternatives. A methodology that provides a two-step solution is developed for this work. First, a heuristic approach is applied to determine the best machine for each process, and then a combined Whale optimization algorithm with a univariate search method is used to allocate optimum tolerances with the best process selection for each sub-stage/operation. The efficiency of the proposed novel methodology is validated by solving two typical tolerance allocation problems of complex assemblies: a wheel mounting assembly and a knuckle joint assembly. Compared with previous approaches, the proposed methodology showed a considerable reduction in tolerance cost and machining time in relatively less computation time.