Background/Objectives: Venous thromboembolism (VTE) is a common and potentially fatal condition in hospitalized patients. Although appropriate risk assessment and prophylaxis reduce VTE events, preventive measures remain underutilized. This study aimed to evaluate the effectiveness of an electronic risk stratification tool within multifaceted interventions for implementing VTE prophylaxis protocols in adult clinical and surgical patients at Hospital Moinhos de Vento, Brazil. Methods: A prospective before-and-after hospital-based study was conducted from 2017 to 2019, including 772 patients admitted to clinical and surgical units for over 48 h. The electronic tool based on the Maynard risk assessment model classified patients’ VTE risk. Padua and Caprini scores served as reference standards for clinical and surgical patients, respectively. Prophylaxis was considered adequate if it complied with institutional protocols. Results: Globally, the Maynard model classified 0.9% as low risk, 76.4% intermediate, and 22.7% high risk, differing notably in orthopedic surgical patients. Overall prophylaxis adequacy was 69.3%, with no significant difference between phases. Orthopedic surgical patients showed a significant decrease in prophylaxis adequacy in phase 2 (p = 0.02). Conclusions: The Maynard model underestimated high-risk classification compared to Padua and Caprini scores, especially in orthopedic surgical patients. Implementation of the electronic tool alongside multifaceted interventions did not improve prophylaxis adequacy.