Background/Objectives: The certification of hospitals as colorectal cancer centers aims to improve treatment quality, but evidence supporting its effectiveness remains limited. This study evaluated the impact of certification on treatment outcomes for rectal cancer patients in Germany. Methods: We conducted a retrospective analysis of 14,905 patients with primary rectal cancer (UICC Stages I-III) treated at 271 hospitals. Treatment outcomes were compared between certified colorectal cancer centers (3624 patients in 55 hospitals) and non-certified hospitals (11,281 patients in 216 hospitals). Additionally, a subset analysis examined outcomes before and after certification within the same institutions. Results: Certified centers demonstrated higher utilization of preoperative imaging (endorectal ultrasound: 70.7% vs. 58.2%, p < 0.001; pelvic MRI: 39.1% vs. 28.5%, p < 0.001) and lower rates of intraoperative complications (4.6% vs. 6.2%, p < 0.001). Surgical quality indicators, including M.E.R.C.U.R.Y. classification (Grade 1: 86.5% both groups, p = 0.620) and anastomotic leakage rates (11.3% vs. 11.9%, p = 0.407), were comparable between certified and non-certified hospitals. Despite treating patients with more favorable tumor stages, certified centers showed no significant advantage in 5-year overall survival (82.8% vs. 82.0%, p = 0.880) or 30-day mortality (2.6% both groups, p = 0.869). Hospital stays were marginally shorter in certified centers (19.46 vs. 20.24 days, p < 0.001). Conclusions: While certification was associated with improved adherence to diagnostic protocols and reduced intraoperative complications, it did not significantly impact surgical quality or long-term survival outcomes. These findings suggest that certification alone may not guarantee superior treatment quality, as hospitals participating in quality assurance programs achieved comparable results without formal certification.