Background: A newly developed, anodized titanium oxide surface containing anatase has been reported to have antimicrobial properties that could reduce bacterial adherence to abutments. Purpose: To investigate if abutments with the anodized surface improve healing and soft tissue health in a randomized controlled study. Materials and Methods: Test abutments with a nanostructured anodized surface were compared with control machined titanium abutments. In total, 35 subjects each received a pair of test and control abutments. The primary endpoint was reduction of biofilm formation at test abutments at the 6‐week follow‐up. Secondary endpoints included several soft tissue assessments. qPCR for gene markers was used to indirectly evaluate healing and soft tissue health. Results: No significant differences in biofilm formation were observed between test and control abutments, but soft tissue bleeding upon abutment removal was significantly lower for test abutments compared with control abutments (P = 0.006) at 6 weeks. Keratinized mucosa height was significantly greater at test abutments compared with control abutments at the 6‐week, 6‐month, and 2‐year follow‐ups. Significant gene expression differences indicated differences in healing and tissue remodeling. Conclusions: Abutments with an anodized and nanostructured surface compared with a conventional, machined titanium surface had no significant effect on bacterial colonization and proteolytic activity but were associated with better soft tissue outcomes such as a lower bleeding index at abutment removal and consistently greater height of keratinized mucosa throughout the 2‐year follow‐up, suggesting improved surface‐dependent peri‐implant healing and soft tissue health.