Objectives The aim of this study was to investigate the influence of real implant‐bed‐specific radiation doses on peri‐implant tissue health in head and neck cancer (HNC) patients after radiotherapy. Material and methods Specific radiation doses in the area of 81 implants, in 15 irradiated HNC patients, were analyzed by matching data from the radiotherapy planning system with those of three‐dimensional follow‐up scans after implantation. Peri‐implant bone resorption was measured radiographically after 1 and 3 years, and peri‐implant tissue health was evaluated clinically. Individual parameters, such as age, gender, and localization, regarding the implant‐specific radiation dose distribution were analyzed statistically. Results The mean implant‐bed‐specific radiation dose was high, with 45.95 Gy to the mandible and 29.02 Gy to the maxilla, but significantly lower than the mean total dose to the tumor bed. Peri‐implant bone resorption correlated with local inflammation and plaque. After 1 year, women temporarily showed significantly more bone loss than men and implant‐specific radiation dose had a significant impact on peri‐implant bone loss after 3 years. Conclusions The presented method is a feasible option to define precise implant‐bed‐specific radiation doses for research or treatment planning purposes. Implant‐based dental restoration after radiotherapy is a relatively safe procedure, but a negative radiation dose‐dependent long‐term effect on peri‐implant bone resorption calls for interdisciplinary cooperation between surgeons and radio‐oncologists to define high‐risk areas.