A system for scheduling the execution of container workloads from a series of applications and a series of containers of each application. The system includes a processor and a non-transitory computer-readable storage medium having instructions stored thereon, which, when executed by the processor, cause the system to calculate a conflict penalty matrix including a conflict penalty for each potential combination of container workloads of the plurality of containers, and calculate a minimum total conflict penalty of the container workloads and a number of workload batches for executing the container workloads. The number of workload batches is associated with the minimum total conflict penalty. The instructions, when executed by the processor, further cause the system to assign the container workloads to the workload batches based on the minimum total conflict penalty and the number of the workload batches.