The present disclosure advantageously provides a computer-based method for partitioning software for an embedded system with a memory protection unit (MPU). Object code within a plurality of object files is converted to intermediate code. A call graph is generated based on the intermediate code. The call graph is transformed into a directed flow graph, which includes updating the call graph's node weights and directed edge weights. The directed flow graph is partitioned into a target number of MPU memory regions, which includes assigning each element of the object code to one of the MPU memory regions. Each element of the object code is relocated to a new object file that corresponds to the assigned MPU memory region. An MPU configuration object file is created that includes one or more configuration parameters for each MPU memory region.