Objectives The marginal quality of ceramic inlays was evaluated after the use of three different instrumental finishing methods in mesio-occluso-distal (mod) cavity boxes in vitro after hydrothermal loading (HTL). Materials and methods Caries-free human molars were divided into three groups. Mod-cavities were conventionally prepared. Box finishing was performed in every group with rotating (RI), sonic (SI), or ultrasonic (USI) instruments. Surface roughness was examined. Twelve mod-cavities remained untreated. Continuous margin quality was evaluated with scanning electron microscopy (SEM). Ceramic inlays were cemented into cavities. After HTL microleakage, marginal and absolute marginal gaps were examined. All data were analyzed statistically. Results Significant differences were found, between cavity surface roughness of RI and SI groups, the RI and USI groups, but not between microleakage, marginal, absolute marginal gaps after HTL and in proximal marginal quality. No correlations between microleakage and marginal gaps nor between microleakage and surface roughness were found. Conclusion Mod-cavity proximal box finishing with SI or USI resulted in a higher surface roughness than the use of RI. The type of the finishing method did not influence the marginal quality of ceramic inlays. For the mod-cavity finishing, the use of SI and USI could be an alternative instrumental method to conventional RI methods with a lower risk of iatrogenic damage of the adjacent teeth. Clinical relevance This study allows the practitioner to better determine the proper indications and limitations of the sonic and ultrasonic instruments for mod-cavity proximal box finishing.