Background Pneumococcal vaccination is an effective preventative measure. However, adult coverage rates remain very low, especially for working-age adults with chronic morbid conditions. Community pharmacists have the potential to improve such vaccination rates, but very little is known about their practices or perspectives. Methods Semistructured interviews were conducted with pharmacists at 12 independently owned community pharmacies purposefully selected from across Alabama. Transcript data were analyzed to identify community pharmacists' knowledge, practices, and perspectives on pneumococcal vaccination for at-risk working-age adults. Results Six major themes were identified regarding community pharmacists' knowledge and practice patterns. Multiple challenges and opportunities to improving vaccination coverage levels were also identified. Several knowledge gaps were noted, and very few pharmacists had provided pneumococcal vaccinations to at-risk adults aged 19 to 64. Most did not fully utilize patient data to identify vaccine candidates, and seldom adopted proactive approaches to promote pneumococcal vaccination. The vaccine was rarely recommended outside of flu season despite year-round vaccine availability. Challenges to increasing vaccination included pharmacy-specific barriers, advocacy, public misperceptions, limited collaboration with area physicians, and resource constraints. Opportunities included capitalizing on the growing acceptance of pharmacy-based immunization, the business case for pneumococcal vaccination, and pharmacists' interest in receiving continuing education. Improving record-keeping systems, pharmacist-patient communication, advocacy, and outreach, and building stronger collaborations with community stakeholders to facilitate the pharmacists' role as immunization advocates were additional areas for improvement. Conclusions Multiple challenges impede increased involvement by community pharmacists in pneumococcal vaccination services; however, opportunities can be exploited to affect such change.