This study aimed to compare polishing systems on color stability, surface roughness, and gloss of additively manufactured permanent and conventional resin composites. Totally 250 disc specimens (6 mm*2 mm) were prepared from resin-based materials [G-ænial Posterior (GP), Clearfil Majesty Esthetic (CME), SonicFill-2 (SF), Tescera (Tes), and Crowntec (CT)]. Following baseline color (ΔE00), gloss (GU), and surface roughness (Ra) measurements, the specimens were randomly divided into 5 groups (n = 10/group) according to polishing systems: Control (mylar strips); OneGloss; OneGloss + Platina Hi-Gloss; OptiDisc; and OptiDisc + Platina Hi-Gloss. Specimens were immersed in coffee for 144 h following polishing. ΔE00, GU, and Ra measurements were repeated. Atomic force microscopy images were taken in all groups. Spearman’s rho correlation coefficient, Robust ANOVA, and Bonferroni correction were used for statistical analysis. Significance level was taken as p < 0.050. Significant differences in ΔE00 values were found among resin-based materials, polishing systems, and their interactions (p < 0.001,p < 0.01, and p = 0.001). Regardless of polishing system, the lowest ΔE00 values were observed in CT, while lowest gloss (GU) values were found in Tes. The lowest surface roughness (Ra) values were detected at OptiDisc group (p < 0.001). A single type of polishing system may not be sufficient to achieve optimal results in resin-based materials.