ObjectiveThe objective of this study is to evaluate the changes at marginal bone level at implants restored with screw‐retained prosthesis connected directly to the implants or with an intermediate abutment, after 3‐year follow‐up.Material and MethodsThirty‐six partially edentulous patients received 72 implants. Each patient received 2 implants and a 2–4‐unit screw‐retained implant‐prosthesis. The test group implants received a screw‐retained prosthesis connected directly to the implant shoulder, the control group prosthesis were connected through a 3‐mm standardised intermediate abutment. Clinical and radiological data were recorded at baseline and at 6‐, 12‐, and 36‐month follow‐up.ResultsAt 36 months, the mean marginal bone loss was 0.13 ± 0.18 mm for the control group and 0.20 ± 0.24 for the test group, with no significant differences between groups (p > .05). Clinical variables (Probing Pocket Depth, Bleeding on Probing and Plaque Index) at 36 months also showed no significant difference between groups. Minor complications frequency was 6.7% in the control group and 5.3% in test group. None of the groups suffered from mayor complications. Patient Reported Outcomes (PROs) showed a General Satisfaction mean score in the control group of 9.40 (SD 0.82) and 9.37 (SD 1.06) in the test group with no significant differences between groups.ConclusionsBone‐level implants restored with screw‐retained partial prostheses with or without intermediate abutments showed similar radiographic and clinical outcomes after 3 years.