Robots operating in space are subject to lower mechanical loads than those on Earth due to the absence of gravity and atmospheric pressure. Reduced force allows for the use of lighter and larger link structures for robots, which, in turn, tend to be more flexible. Modeling and simulation of flexible structures incur high computational demands that are sometimes prohibitive to inform an autonomous control or decision-making algorithm in a timely manner. Therefore, efficient model order reduction (MOR) techniques that accelerate simulation and execution times while maintaining their fidelity to provide a suitable output are required. This paper introduces the energy-based MOR for Flexible In-Space (eMORFIS) Robotic Systems method. The proposed eMORFIS is based on Euler–Bernoulli beam theory and finite element discretization, seamlessly incorporates both internal and external forces while supporting revolute and prismatic joints. The resulting structural dynamics are projected into modal space, where MOR techniques generate reduced models that preserve essential dynamic behavior while enhancing computational performance. The eMORFIS methodology is demonstrated with one- and two-degree-of-freedom planar manipulators, and its extension to multi-link systems is straightforward. This proposed approach is validated in a simulation environment using flexible and rigid links in robotic systems. The results show a significant reduction in the model’s order, while maintaining millimetric differences in tip position and orientation between the full and reduced model