This paper addresses the multi-objective optimization problem arising in the operation of heat integrated batch plants, where makespan and utility consumption are the two conflicting objectives. A new continuous-time MILP formulation with general precedence variables is proposed to simultaneously handle decisions related to timing, product sequencing, heat exchanger matches (selected from a two-stage superstructure) and their heat loads. It features a complex set of timing constraints to synchronize heating and cooling tasks, derived from Generalized Disjunctive Programming. Through the solution of an industrial case study from a vegetable oil refinery, we show that major savings in utilities can be achieved while generating the set of Pareto optimal solutions through the 6-constraint method. (C) 2015 Elsevier Ltd. All rights reserved.