OBJECTIVE: This study investigated the bonding performance of three universal adhesive systems applied using etch-and-rinse (ER) or self-etch (SE) strategies on natural dentin caries. MATERIALS AND METHODS: Sixty human third molars were selected for this study: 30 naturally carious (CAD) and 30 sound (SD) teeth. The dentin surfaces were exposed, and teeth were randomly assigned to each evaluated adhesive system: Scotchbond Universal (SBU), Futurabond U (FBU), and Prime&Bond Elect (PBE) and an adhesive strategy: ER or SE. The adhesive systems were applied following the manufacturer's instructions, and the teeth were restored using a resin composite (Filtek Supreme Ultra, 3M). After 24 hours (distilled water at 37°C), samples were sectioned and evaluated using microtensile bond strength analysis (µTBS), micro-Raman spectroscopy to evaluate the degree of conversion within the hybrid layer (DC), and scanning electronic microscopy (SEM) to describe the morphology of the hybrid layer. The µTBS and DC data were analyzed using three-way analysis of variance and Tukey's test for means comparison (α=0.05). The SEM images were analyzed qualitatively. RESULTS: Reduced µTBS values were observed when comparing CAD with SD, regardless of adhesive system or strategy (p<0.0001). SBU showed statistically higher µTBS for both dentin substrates and strategies (p<0.0001). Furthermore, SBU showed greater integrity of the hybrid layer and resin tag formation compared with FBU and PBE. Mean µTBS values for FBU were higher for SD in the SE mode, whereas higher mean µTBS values were observed for CAD in the ER mode, both compared with PBE (p<0.001). CONCLUSION: Bonding performance is reduced on a caries-affected substrate. The ER strategy was not able to improve the bonding performance on natural CAD for universal adhesive systems. Improved bonding performance was obtained when using the Scotchbond Universal system.