Maintaining the quality of breathing air in urban and industrial areas is one of the biggest challenges faced by humanity in the modern era. Diesel engines, as one of the main providers of energy supply for modern equipment and transport, are also unfortunately contributing highly to the deterioration of air quality. A recent research path on the limitation of diesel engine emissions is the use of alternative fuel from vegetable or animal fats or oil called biodiesel. Although the use of biodiesel has proven its efficiency in reducing emissions, it remains a problem to maintain the engine’s efficiency when shifting to biodiesel, especially due to its injection and atomization properties; most of the recent research focused on improving biodiesel fuel quality by blending it with traditional diesel fuel, but few works can be found on the regulation or control of diesel engine process when shifting to 100% biodiesel fuel (B100). This work proposes a fuel control strategy and methodology based on diesel engine operating data obtained from an experimentally designed rate of injection model (ROI) at different injection pressures and a jet and spray droplet distribution validated a two-zone model. Results show that B100 gives a higher amount of about 8% of injected fuel, a longer jet penetration of about 20 mm higher at 100 MPa injection pressure, a wider cone angle, and about a 40% increase of coarseness of the jet distribution. The experimental and numerical-based control strategy provides interacting relationships between B100 properties and specific engine features where actions shall be made to keep the engine’s efficiency when the shift is made; meanwhile, the algorithm provides a hierarchical step-by-step correcting procedure taking into account the possible degradation that could occur from the use of B100 in diesel engines.