Background: Prophylactic polishing pastes (PPPs) are widely used to clean teeth and dental restorations; however, their effects on restorative materials are crucial for clinical outcomes. This study investigates the impact of PPPs on the susceptibility of CAD/CAM restorative materials to staining and the relationship between surface roughness and discoloration. Methods: Samples of tested materials (resin nanoceramic, hybrid ceramic, feldspathic ceramic, and lithium disilicate-reinforced glass ceramic) were treated with various PPPs (Cleanic, CleanJoy, Detartrine, Proxyt). Surface roughness and color parameters were recorded before and after the PPP application and following coffee immersion for 12 days. Initial measurements of surface roughness (Ra1) and color were taken. The specimens were divided into groups based on the PPP applied. After PPP application, secondary roughness (Ra2) and color values were measured. Changes in roughness (Delta Ra), color (Delta E*ab, Delta E00), and whiteness index (Delta WID) were calculated post-application and after coffee immersion. Data normality was tested with the Shapiro-Wilks test. Two-way ANOVA evaluated the effects of material type and PPP on Delta E, Delta WID, and Delta Ra. One-way ANOVA, Tukey HDS test, and Pearson correlation were used for further analysis, with significance set at p < 0.05. Results: The Vita Enamic-Detartrine group showed the highest Delta Eab 1 and Delta E001 values, while Cerasmart-control showed the lowest. The Vita Enamic-Proxyt group had the lowest Delta WID1, and Vita Enamic-Cleanjoy exhibited the highest values of Delta Eab 2, Delta E002, and Delta WID2. The E.MAX-control group had the lowest values for these metrics. No significant correlation was found between Delta Ra and color changes (Delta E*ab 2, Delta E002, Delta WID2); however, a moderate positive correlation was found between values of Delta E1 and Delta E2. Conclusions: These findings indicate that PPPs significantly affect the discoloration and surface features of CAD/CAM materials, with both types of PPPs and materials.