This cross-sectional study aimed to identify and quantify up to 42 target species colonizing the early biofilm of dental implants restored with titanium or zirconia abutments. A total of 720 samples from 20 healthy individuals were investigated. Biofilm samples were collected from the peri-implant sulci, inner parts of implants, abutment surfaces and prosthetic crowns over a functioning period of 30 days. Checkerboard DNA-DNA hybridization was used for microbial detection and quantitation. Clinical characteristics (probing depth, bleeding on probing, clinical attachment level and marginal bone loss) were also investigated during the monitoring period. Genome counts were low at the implant loading time point for both the abutment materials, and increased over time. Both the titanium and the zirconia groups presented similar microbial counts and diversity over time, and the microbiota was very similar to that colonizing the remaining teeth. Clinical findings were consistent with a healthy condition with no significant difference regarding marginal bone loss between the two materials.