In-situ bioremediation is a cost-effective technique to eliminate petroleum hydrocarbons from groundwater. In previous studies, this has been mostly applied under the approximation of a homogeneous porous medium, even though in reality aquifers are often characterized by significant heterogeneities. Here, different heterogeneous and equivalent homogeneous hydraulic conductivity fields are considered to study the effect of aquifer heterogeneity on optimal in-situ bioremediation. For this, the multiobjective simulation-optimization (S/O) model referred to as BIOEFGM-NSGA II is proposed — which uses the element-free Galerkin method (EFGM) for discretization of the governing equations, and the non-dominated sorting genetic algorithm II (NSGA II) for multiobjective optimization. This model is then applied to different heterogeneous conductivity fields generated through a pseudo-random correlated field generator for different combinations of variance and correlation lengths with constant mean. Results show that the optimal pumping policy for an equivalent homogeneous conductivity field violates the constraint of maximum allowable concentration in all the studied heterogeneous fields. To satisfy this constraint, in-situ bioremediation cost increases by 8.47% to 56.83% to that of a homogeneous field. It shows the significance of aquifer heterogeneity in designing an optimized in-situ bioremediation system and hence, should be incorporated in the S/O model for in-situ groundwater bioremediation.