The most frequently occurring adverse events in individuals with a transfemoral amputation treated with a bone-anchored prosthesis are soft tissue infections and stoma-related complications. These soft tissue complications are believed to be influenced by surgical technique and implant design, but little is known about the effect of changes to treatment on these events. (1) What is the result of surgical technique and implant modifications on the incidence of soft tissue infections and stoma-related complications in transfemoral bone-anchored prosthesis users, depending on whether they had a conventional stoma and a cobalt-chrome-molybdenum (CoCrMo) osseointegration implant (treatment period 2009 to 2013) or a shallower stoma and titanium osseointegration implant (2015 to 2018)? (2) What is the incidence of serious complications, such as bone or implant infection, aseptic loosening, intramedullary stem breakage, and periprosthetic fracture? Between 2009 and 2013, we performed osseointegration implant surgery using a conventional surgical technique and a CoCrMo implant in 42 individuals who had a lower extremity amputation experiencing socket-related problems that resulted in limited prosthesis use. We considered all individuals treated with two-stage surgery with a standard press-fit transfemoral osseointegration implant as potentially eligible for inclusion. Based on this, 100% (42) were eligible, and 5% (two of 42) were excluded because they did not provide informed consent, leaving 95% (40 of 42) for analysis. Between 2015 and 2018, we treated 79 individuals with similar indications with osseointegration implant surgery, now also treating individuals with dysvascular amputations. We used an adapted surgical technique resulting in a shallower stoma combined with a titanium implant. Using the same eligibility criteria as for the first group, 51% (40 of 79) were eligible; 49% (39 of 79) were excluded because they were treated with transtibial amputation, a patient-specific implant, or single-stage surgery and 1% (one of 79) were lost before the 2-year follow-up interval, leaving 49% (39 of 79) for analysis. The period of 2013 to 2015 was a transitional period and was excluded from analysis in this study to keep groups reasonably comparable and to compare a historical approach with the present approach. Hence, we presented a comparative study of two study groups (defined by surgical technique and implant design) with standardized 2-year follow-up. The risk factors for adverse events were similar between groups, although individuals treated with the shallow stoma surgical technique and titanium implant potentially possessed an increased risk because of the inclusion of individuals with dysvascular amputation and the discontinuation of prolonged postoperative antibiotic prophylaxis. Outcomes studied were soft tissue infections and stoma-related complications (hypergranulation or keloid formation as well as stoma redundant tissue) and bone or implant infection, aseptic loosening, implant stem breakage, periprosthetic fracture, and death. Patients treated with the shallow stoma surgical technique and titanium implant experienced fewer soft tissue infections (13 versus 76 events, absolute risk 0.17 [95% CI 0.09 to 0.30] versus 0.93 [95% CI 0.60 to 1.45]; p < 0.01), which were treated with less invasive measures, and fewer stoma redundant tissue events (0 versus five events, absolute risk 0 versus 0.06 [95% CI 0.03 to 0.14]) than patients treated with the conventional stoma surgical technique and CoCrMo implant. This was contrasted by an increased incidence of surgical site infections occurring between surgical stages 1 and 2, when no stoma was yet created, after the implementation of treatment changes (conventional surgery and CoCrMo implant versus shallow stoma surgery and titanium implant: one versus 11 events, absolute risk 0.01 [95% CI 0.00 to 0.08] versus 0.14 [95% CI 0.08 to 0.25]; p = 0.02). Patients treated with the shallow stoma surgical technique and titanium implant did not experience serious complications, although bone infections occurred (six events in 8% [three of 40] of patients) in the conventional surgery and CoCrMo implant group, all of which were successfully treated with implant retention. Adaptations to surgical technique and newer implant designs, as well as learning curve and experience, have resulted in a reduced incidence and severity of soft tissue infections and stoma redundant tissue, contrasted by an increase in surgical site infections before stoma creation. Serious complications such as deep implant infection were infrequent in this 2-year follow-up period. We believe the benefits of these treatment modifications outweigh the disadvantages and currently advise surgeons to create a shallower stoma with a stable soft tissue envelope, combined with a titanium implant. Level III, therapeutic study.