HORUS is a low-cost reconfigurable CubeSat computing architecture built from commercial off-the-shelf (COTS) FPGA hardware and integrated with NASA Goddard’s core Flight System (cFS). The proposed system targets distributed CubeSat cluster and swarm missions through a master-worker architecture in which a master node coordinates multiple worker nodes using lightweight orchestration software for task allocation, health monitoring, and network reconfiguration. The central capability of HORUS is in-flight partial reconfiguration, which allows individual FPGA nodes to load and swap specialized hardware modules during operation to adapt to changing mission requirements under limited onboard power and resource constraints. To demonstrate integration beyond computing alone, each node also supports a closed-loop brushless DC reaction wheel subsystem through FPGA logic, a MicroBlaze soft processor, an electronic speed controller, and custom RTL, enabling practical hardware-assisted attitude-control support using discrete and readily available components. In addition, the architecture considers FPGA-based Quadrature Phase Shift Keying (QPSK) for robust internode communication. Together, these subsystems establish a COTS-based framework that bridges reconfigurable hardware, flight software, distributed orchestration, and onboard control for adaptable and low-cost CubeSat computing.