Recently, many studies are carried out with inspirations from ecological phenomena for developing optimization techniques. The new algorithm that is motivated by a common phenomenon in agriculture is colonization of invasive weeds. In this paper, a modified invasive weed optimization (IWO) algorithm is presented for optimization of multiobjective flexible job shop scheduling problems (FJSSPs) with the criteria to minimize the maximum completion time (makespan), the total workload of machines and the workload of the critical machine. IWO is a bio-inspired metaheuristic that mimics the ecological behaviour of weeds in colonizing and finding suitable place for growth and reproduction. IWO is developed to solve continuous optimization problems that’s why the heuristic rule the Smallest Position Value (SPV) is used to convert the continuous position values to the discrete job sequences. The computational experiments show that the proposed algorithm is highly competitive to the state-of-the-art methods in the literature since it is able to find the optimal and best-known solutions on the instances studied.