To investigate the effects of phospholipids (PLs) in chocolate, model systems were designed by adding 0.3%, 0.5%, and 0.8% (w/w) phosphatidylcholine (PC), phosphatidylethanolamine (PE), and phosphatidylserine (PS) to the control system (0.0% PL). Bloom behaviors were quantified by changes in whiteness index (ΔWI), white area percentage (WA%) and surface morphology over 28-day accelerated storage. Bloom was significantly retarded in all PL systems (p < 0.0001), especially showing almost no visual bloom in PE and PS systems during 28-day storage: ΔWI was reduced to below 1.5 (16.97 for the control) and WA% was reduced to below 10% (99.47% for the control). This reduction in bloom was further confirmed by low surface roughness and porosity. Particle interactions (quantified by Casson viscosity and sedimentation volume) were significantly reduced (p < 0.0001) and amount of crystallization (quantified by differential scanning calorimetry and oscillatory rheology) were significantly increased in all PL systems (p < 0.05). These results suggest that PLs can improve the microstructural stability of the nonfat particle phase and the crystalline fat phase, thereby reducing fat migration and preventing bloom formation.