Objective Despite the positive attitudes pharmacists have toward evidence-based practices (EBPs), its application in community pharmacies in Saudi Arabia is lacking. Therefore, this study aimed to explore and assess EBPs by community pharmacists in Saudi Arabia when they dispense over-the-counter (OTC) medications for three minor ailments: diarrhea, cough, and the common cold. Research design and methods We used a mixed-methods approach consisting of two study parts. The first was a quantitative investigation that used mystery shoppers. Four researchers, posing as mystery shoppers, visited 214 randomly selected pharmacies in the Riyadh region of Saudi Arabia. They used 14 questions from a standardized checklist to examine EBPs by community pharmacists. The qualitative part of the study entailed three focus-group discussions with 13 pharmacists from different community practice settings and explored factors that affected the application of EBPs when supplying OTC medications from the pharmacists’ point of view. Results The analysis indicated that 40% of pharmacists dispensed OTC medications according to EBPs. Logistic regression analysis showed that one question, "Describe your symptoms", predicted the correct supply of OTC medications (p = 0.021). The qualitative section of the study identified nine factors that affected EBP. Some of these factors facilitated EBP, such as established patient-pharmacist relationships, some acted as barriers such as conflicts between available evidence, while other factors could either facilitate or hinder EBPs, such as the health literacy of the patient. Conclusion Given that dispensing OTC medication is a core function of pharmacists, this study uncovered low adherence to EBPs by community pharmacists in Saudi Arabia when dispensing OTC medication for three minor ailments: diarrhea, cough, and the common cold. Furthermore, this study identified a number of explanatory factors for this low adherence. Targeting these factors could help change the behavior of pharmacists and decrease undesirable outcomes.