Background: In 2015, the Directorate General of Drug Administration (DGDA) of Bangladesh accredited model pharmacies (MPs) to enhance the quality of pharmacy services across the country. We examined the challenges and opportunities for pharmacists in MPs, and also explored the perspectives of the pharmacy stakeholders for improving good pharmacy practices (GPPs) in Bangladesh. Methods: In-depth interviews (IDIs) were conducted with graduate pharmacists (Grade A) and diploma pharmacists (Grade B) recruited from a few selected MPs that were included in a previous study. Key informant interviews (KIIs) were conducted with the government and non-government stakeholders who were involved in pharmacy regulations and practices. Trained qualitative researchers conducted IDIs and KIIs using interview topic guides under relevant themes developed by the study investigators. Results: Between February and March 2021, nine Grade A and six Grade B pharmacists and nine government and non-government stakeholders were interviewed. The key challenges, as well as demotivational factors, for Grade A pharmacists were reported to be multiple responsibilities, inadequate salary, poor social status, an unfavorable working environment, long working hours, a lack of recognition, and low respect for their profession. However, Grade B pharmacists expressed job satisfaction, primarily due to working opportunities in reputable pharmacies and learning opportunities. The stakeholders reported a high operation cost of the MPs, a shortage of trained pharmacists, poor salary structures, and a lack of public awareness about the critical roles of the pharmacists in healthcare to be challenges of retaining Grade A pharmacists at the MPs. Addressing the challenges of the pharmacists and revising compensation packages along with strengthening monitoring systems would be important for improving GPPs at the MPs. Conclusions: This study has demonstrated that specifying the roles of the pharmacists, offering competitive packages, conducive working hours, and professional recognition would be imperative for the retention of trained pharmacists at MPs. Implementing regulatory standards and monitoring performance would enhance good pharmacy practices in Bangladesh.