To analyse the soft tissue morphology under healthy and experimental mucositis conditions comparing zirconia and titanium implants. Forty-two patients with two adjacent missing teeth received one zirconia (Zr) and one titanium (Ti) implant, with the mesial and distal position randomized. At 3months, half of the patients were instructed to continue (healthy; h) and the other half to omit (experimental mucositis; m) oral hygiene around the implants for 3weeks. Clinical parameters were evaluated before and after the experimental phase, and a soft tissue biopsy was harvested. Mixed model analyses were performed to analyse the data. The plaque control record increased significantly for the two mucositis groups, reaching 68.3±31.9% (mean ± SD) for Zr-m and 75.0±29.4% for Ti-m (p<.0001), being also significantly lower for Zr-m than for Ti-m. Bleeding on probing remained stable in group Zr-m and amounted to 21.7±23.6%, but increased significantly in group Ti-m (p=.040), measuring 32.5±27.8%. The number of inflammatory cells and the length of the junctional epithelium did not significantly differ between the groups. Both implants rendered similar outcomes under healthy conditions. Lower plaque and bleeding scores were detected for zirconia implants under experimental mucositis conditions. Histologically, only minimal differences were observed.