Evidence suggests that community pharmacy service quality varies, and that this may relate to pharmacy ownership. However little is known about wider organisational factors associated with quality. To investigate organisational factors associated with variation in safety climate, patient satisfaction and self-reported medicines adherence in English community pharmacies. Multivariable regressions were conducted using data from two cross-sectional surveys, of 817 pharmacies and 2124 patients visiting 39 responding pharmacies, across 9 diverse geographical areas. Outcomes measured were safety climate, patient satisfaction and self-reported medicines adherence. Independent variables included service volume (e.g. dispensing volume), pharmacy characteristics (e.g. pharmacy ownership), patient characteristics (e.g. age) and areal-specific demographic, socio-economic and health-needs variables. Valid response rates were 277/800 (34.6%) and 971/2097 (46.5%) for pharmacy and patient surveys respectively. Safety climate was associated with pharmacy ownership (F8,225 = 4.36, P < 0.001), organisational culture (F4, 225 = 12.44, P < 0.001), pharmacists' working hours (F4, 225 = 2.68, P = 0.032) and employment of accuracy checkers (F4, 225 = 4.55, P = 0.002). Patients' satisfaction with visit was associated with employment of pharmacy technicians (β = 0.0998, 95%CI = [0.0070,0.1926]), continuity of advice-giver (β = 0.2593, 95%CI = [0.1251,0.3935]) and having more reasons for choosing that pharmacy (β = 0.3943, 95%CI = [0.2644, 0.5242]). Satisfaction with information received was associated with continuity of advice-giver (OR = 1.96, 95%CI = [1.36, 2.82]), weaker belief in medicines overuse (OR = 0.92, 95%CI = [0.88, 0.96]) and age (OR = 1.02, 95%CI = [1.01, 1.03]). Regular deployment of locums by pharmacies was associated with poorer medicines adherence (OR = 0.50, 95%CI = [0.30, 0.84]), as was stronger patient belief in medicines overuse (OR = 0.88, 95%CI=[0.81, 0.95]) and younger age (OR = 1.04, 95%CI = [1.01, 1.07]). No patient outcomes were associated with pharmacy ownership or service volume. This study characterised variation in the quality of English community pharmacy services identifying the importance of skill-mix, continuity of care, pharmacy ownership, organisational culture, and patient characteristics. Further research is needed into what constitutes and influences quality, including the development of validated quality measures.