Background/Objectives: Physical exercise (PE) is essential in promoting health and quality of life and protecting against chronic diseases. Health professionals are identified as key figures in promoting and prescribing PE, yet various factors may impact this during consultations. This study aims to assess Portuguese specialist physicians’ understanding of the importance of PE prescriptions. It will also investigate the approaches they utilize in promoting and prescribing PE, their knowledge of incorporating this practice into their consultations, and the major facilitators or barriers to prescription. Methods: A cross-sectional observational study was conducted using a validated questionnaire distributed via email by the Centre Regional Section of the Portuguese Medical Association to physicians. The data were analyzed using descriptive and inferential statistics. Results: In total, 414 responses were collected, with participants representing different medical specialties. The participants were primarily women (62.8%) with a mean age of 49.9 ± 14.9 years. While 85.5% of physicians promoted and prescribed PE, recognizing its cardiovascular and metabolic health benefits, only 24.0% received specific training, and 73.7% were unaware of relevant guidelines. Older male physicians (over 60 years old) expressed more confidence in PE prescriptions, while younger ones were more familiar with electronic prescribing tools. Identified barriers included patient compliance (42.3%), a lack of accessible PE resources (18.4%), and limited consultation time (17.4%). Most physicians (64.4%) relied on oral counseling for prescriptions. Conclusions: Most Portuguese specialist doctors recognize the benefits of PE prescriptions. However, barriers like inadequate training and patient compliance hinder PE implementation. Enhanced training and resources are vital for effectively integrating PE into clinical practice.