Background: Acellular matrices (AM) might enable a direct single-stage breast reconstruction procedure resulting in an improved efficacy of the reconstruction phase for patients. Safety concerns are an important issue due to a recent study which shows that single-stage breast reconstruction with Strattice™ resulted in more complications versus a two-stage reconstruction. Therefore, the goal of this study is to compare the short- and long-term complications of a single-stage breast reconstruction with the use of two types of AM (Strattice™ and Meso Biomatrix®) versus two-stage breast reconstruction without the use of an AM. Methods: Cohort study with single-stage breast reconstruction with Strattice™ (n = 28) or Meso BioMatrix® (n = 20) or two-stage breast reconstruction without an AM (n = 36) at the Maastricht Academic Hospital, the Netherlands. All complications, in particular major complications with the need for re-admission to the hospital, re-exploration, and implant explantation, were the primary outcome measures. A 1-year follow-up was achieved for all patients. Results: Baseline characteristics of all 52 patients were similar between groups. There was a significantly higher complication rate in the single-stage AM groups with loss of the implant in 40.0% of the breasts from the Meso BioMatrix® group and in 10.7% of the Strattice™ group compared to no implant loss in the control group. Conclusions: This cohort study clearly suggests that the use of a single-stage breast reconstruction is not safe with the use of these AMs. Well-designed prospective studies that guarantee the safety of those matrices should be published before these AMs are used in implant-based surgery. Level of Evidence: Level III, risk / prognostic study.