This study evaluated the bond strength of relining materials to different denture base materials polyamide and polymethylmethacrylate denture base materials after various surface conditioning methods. Denture base resin specimens (N = 128; n = 8 per group) (10 × 10 × 2.5 mm3) were fabricated out of injection-moulded thermoplastic polyamide resin (POL) (Deflex) and heat-polymerized polymethylmethacrylate (PMMA, Dura Dent) (HC). The specimens were randomly divided into 4 main groups according to different surface conditioning methods: (a) No conditioning, control (C), (b) grinding with green stone (G), (c) application of primer (V), (d) silica coating with Al2O3 particles coated with SiO2 (Rocatec) (R). Half of the specimens in each group received auto-polymerized hard relining resin (GC, GC Reline Hard) and the other half PMMA based relining resin (SC, Dura Dent). After thermocycling (×5000), the bonded specimens were tested under tensile forces (0.5 mm/min). Data (MPa) were analyzed using Mann–Whitney U and Kruskal–Wallis tests (alpha = 0.05). Bond strength of relining resins were significantly higher to PMMA than to POL, regardless of the conditioning method (p < 0.05). While R positively affected the bond strength results (p < 0.05) (4.99 ± 1.65–3.27 ± 1.31), application V or G did not show significant effect to POL-relining resin adhesion. After R conditioning, bond strength values were significantly higher in HC-GC group (7.48 ± 2.32) than POL-GC group (3.27 ± 1.31) (p < 0.05). Adhesion of auto-polymerized relining materials to thermoplastic polyamide or polymethylmethacrylate denture resins could be improved after surface conditioning with silica-coating.