Objective We aim to investigate pharmacies’ dispensing behaviour under the existing dispensing regulations in Germany. Methods Using administrative data, we performed a cross-sectional retrospective study to analyse whether the competitive environment and pharmacy characteristics, i.e., organisation, lead to dispensing choices aimed at by third-party payers. We specified generalised linear models with the share of imported pharmaceuticals, generic share, and share of preferred brands as dependent variables. Results The final dataset contained 49,260,902 prescriptions from 16,797 pharmacies. The average share of imported pharmaceuticals across the pharmacies was 18.4% (standard deviation (SD) 8.8), the average generic share was 92.8% (SD 2.1), and compliance with preferred brands was 81.3% (SD 5.9). Pharmacies with little competition used fewer imported pharmaceuticals (p < 0.001), generics (p < 0.001) and preferred brands (p < 0.001); less organised pharmacies yielded similar results. The difference in outcomes between pharmacies in the first and 4th quartiles of the pharmacy organisation variable is 17.4% vs. 17.0% for share of imported pharmaceuticals, 92.8% vs. 92.7% for generic share and 81.9% vs. 81.1% for compliance with preferred brands. Conclusion We show that pharmacies’ dispensing choices meet the aims of payers at high levels. However, dispensing behaviour varies between pharmacies. Increasing competition among pharmacies and targeting pharmacies with high shares of bill auditing seem viable options to improving dispensing behaviour as defined by payers.