We present an open-source software package, MISTER-T (Manipulating an Interacting System of Total Electrons in Real-Time), for the quantum optimal control of interacting electrons within a time-dependent Kohn-Sham formalism. In contrast to other implementations restricted to simple models on rectangular domains, our method enables quantum optimal control calculations for multi-electron systems (in the effective mass formulation) on nonuniform meshes with arbitrary two-dimensional cross-sectional geometries. Our approach is enabled by forward and backward propagator integration methods to evolve the Kohn-Sham equations with a pseudoskeleton decomposition algorithm for enhanced computational efficiency. We provide several examples of the versatility and efficiency of the MISTER-T code in handling complex geometries and quantum control mechanisms. The capabilities of the MISTER-T code provide insight into the implications of varying propagation times and local control mechanisms to understand a variety of strategies for manipulating electron dynamics in these complex systems. Program summaryProgram Title: MISTER-TCPC Library link to program files:https://doi.org/10.17632/psymy4ddnw.1Licensing provisions: GNU General Public License 3Programming language: MATLABSupplementary material: animated movies of total electron densities under the influence of optimal control fields for (1) an asymmetric double-well potential for long propagation times, (2) an asymmetric double-well potential for short propagation times, and (3) a triple-well potential with a position-dependent effective mass.Nature of problem: The MISTER-T code solves quantum optimal control problems for interacting electrons within a time-dependent Kohn-Sham formalism. It can handle two-dimensional systems with arbitrary cross-sectional geometries within the effective mass formulation. The user-friendly code uses forward and backward propagator integration methods to evolve the Kohn-Sham equations with a pseudoskeleton decomposition algorithm for enhanced computational efficiency.Solution method: iterative solution of the quantum optimal control equations using finite element methods, effective mass formulation, pseudoskeleton decomposition, sparse matrix linear algebra, and nonuniform fast Fourier transforms.