Background: Since 1 January 2004, all physicians, psychotherapists, and medical care centers that are under contract to statutory healthcare in Germany are obliged, according to § 135a Section 2 of the Fifth Social Security Statute Book, to introduce an intra-institutional quality management system. Methods: A total of 24 medical practices were chosen through random sampling. In total, there were 12 family physicians and specialist practices each and eight practices each per quality management system. The analysis was carried out with the help of three specially developed questionnaires (physician, employee, and patient). A total of 26 quality categories with different questions were available in the three survey groups (physicians, employees, and patients). The Kruskal–Wallis test checked the extent to which the different scores between the quality management systems were significant and effective for specialists or family physicians. Results: ”Quality and Development in Practices (QEP)” had the highest average score. Due to a specific family practitioner specialism, “Quality management in Saxony medical practices (QisA)” followed with good average scores. The individual quality categories in the quality management systems, such as the “range of services” or “allocation of appointments”, received the highest average scores among the specialists. In contrast, categories such as “telephone enquiries” and “external cooperation and communication” received the highest average scores among the family physicians. Conclusion: Differences in the evaluation of quality management systems and medical groups (specialists/family physicians) were found in the study. The reasons for these differences could be found in the quality categories.