Purpose: Complex, involuntary, non-periodic, deformable motion presents a confounding factor to cone-beam CT (CBCT) image quality due to long (>10 s) scan times. We report and demonstrate an image-based deformable motion compensation method for CBCT, including phantom, cadaver, and animal studies as precursors to clinical studies. Methods: The method corrects deformable motion in CBCT scan data by solving for a motion vector field (MVF) that optimizes a sharpness criterion in the 3D image (viz., gradient entropy). MVFs are estimated by interpolating M locally rigid motion trajectories across N temporal nodes and are incorporated in a modified 3D filtered backprojection approach. The method was evaluated in a cervical spine phantom under flexion, and a cadaver undergoing variable magnitude of complex motion while imaged on a mobile C-arm (Cios Spin 3D, Siemens Healthineers, Forchheim, Germany). Further assessment was performed on a preclinical animal study using a clinical fixed-room C-arm (Artis Zee, Siemens Healthineers, Forchheim, Germany). Results: In phantom studies, the algorithm resolved visibility of cervical vertebrae under situations of strong flexion, reducing the root-mean-square error by 60% when compared to a motion-free reference. Reduced motion artifacts (blurring, streaks, and loss of soft-tissue edges) were evident in abdominal CBCT of a cadaver imaged during small, medium, and large motion-induced deformation. The animal study demonstrated reduction of streaks from complex motion of bowel gas during the scan. Conclusion: Overall, the studies demonstrate the robustness of the algorithm to a broad range of motion amplitudes, frequencies, data sources (i.e., mobile or fixed-room C-arms) and other confounding factors in real (not simulated) experimental data (e.g., truncation and scatter). These preclinical studies successfully demonstrate reduction of motion artifacts in CBCT and support translation of the method to clinical studies in interventional body radiology.