Animal bones, particularly from cattle after slaughter, are commonly discarded, posing environmental challenges and highlighting the need for sustainable valorization. This study investigated the effect of enzyme and organic acid treatment on physicochemical properties, particle size, microstructure and safety of meat-bone paste (MBP). Two samples were prepared: a control (MBP-C) without enzyme treatment and an experimental sample (MBP-E) treated with pepsin and ascorbic acid. Results showed that the enzyme reaction rate increased from 0.004 mmol/min at 60 min to 0.014 mmol/min at 120–180 min before declining to 0.006 mmol/min at 480 min, suggesting substrate depletion or product inhibition. Temperature greatly influenced reaction rates, peaking at 0.0129 mmol/min at 30 °C, with significant declines at higher temperatures due to enzyme denaturation. The enzyme’s kinetic performance was proportional to the pepsin concentration, demonstrating enhanced catalytic efficiency at higher enzyme concentrations. Particle size analysis revealed that enzyme treatment significantly reduced bone particle size, with 86.33% of particles measuring between 0.05 and 0.2 mm, compared to 86.4% between 0.25 and 0.75 mm in the untreated sample. Microscopy confirmed these findings, showing an average particle size reduction from 0.21 mm to 0.052 mm after enzyme treatment. Physicochemical analysis revealed no significant differences in chemical composition between the two samples. However, enzyme-treated MBP-E exhibited a lower pH (5.9) compared to MBP-C (7.02), attributed to the addition of ascorbic acid. Water-binding capacity significantly increased in MBP-E (82.54% vs. 77.28%), indicating enhanced hydration and collagen loosening during enzymatic action. Enzyme treatment significantly reduced the total viable count and eliminated pathogenic bacteria (E. coli, Listeria, Salmonella), improving MBP safety. These findings highlight the potential of this approach for valorizing animal bones as a valuable food ingredient while promoting sustainable waste management practices.