(1) Introduction: In response to patient concerns about breast cancer recurrence, increased use of breast magnetic resonance imaging and genetic testing, and advancements in breast reconstruction techniques, mastectomy rates have been observed to rise over the last decade. The aim of the study is to compare the outcomes of prepectoral and subpectoral implants and long-term, dual-stage resorbable mesh-based breast reconstructions in mutation carriers (prophylactic surgery) and breast cancer patients. (2) Patients and methods: This retrospective, two-center study included 170 consecutive patients after 232 procedures: Prepectoral surgery was performed in 156 cases and subpectoral was performed in 76. (3) Results: Preoperative chemotherapy was associated with more frequent minor late complications (p < 0.001), but not major ones (p = 0.101), while postoperative chemotherapy was related to more frequent serious (p = 0.005) postoperative complications. Postoperative radiotherapy was associated with a higher rate of minor complications (31.03%) than no-radiotherapy (12.21%; p < 0.001). Multivariate logistic regression found complications to be significantly associated with an expander (OR = 4.43), skin-reducing mastectomy (OR = 9.97), therapeutic mastectomy vs. risk-reducing mastectomy (OR = 4.08), and postoperative chemotherapy (OR = 12.89). Patients in whom prepectoral surgeries were performed demonstrated significantly shorter median hospitalization time (p < 0.001) and lower minor complication rates (5.77% vs. 26.32% p < 0.001), but similar major late complication rates (p = 0.915). (4) Conclusions: Implant-based breast reconstruction with the use of long-term, dual-stage resorbable, synthetic mesh is a safe and effective method of breast restoration, associated with low morbidity and good cosmesis. Nevertheless, prospective, multicenter, and long-term outcome data studies are needed to further evaluate the benefits of such treatments.