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. 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 (ΔRa), color (ΔEab, ΔE00), and whiteness index (ΔWID) 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 ΔE, ΔWID, and ΔRa. One-way ANOVA, Tukey HDS test, and Pearson correlation were used for further analysis, with significance set at < 0.05. The Vita Enamic-Detartrine group showed the highest ΔEab 1 and ΔE001 values, while Cerasmart-control showed the lowest. The Vita Enamic-Proxyt group had the lowest ΔWID1, and Vita Enamic-Cleanjoy exhibited the highest values of ΔEab 2, ΔE002, and ΔWID2. The E.MAX-control group had the lowest values for these metrics. No significant correlation was found between ΔRa and color changes (ΔEab 2, ΔE002, ΔWID2); however, a moderate positive correlation was found between values of ΔE1 and ΔE2. These findings indicate that PPPs significantly affect the discoloration and surface features of CAD/CAM materials, with both types of PPPs and materials.