When providing comprehensive medication management (CMM) services, pharmacists must recognize patients’ medication experiences to make patient-centered decisions. The aim of this study was to understand how patients’ medication experiences are applied in pharmacists’ decision-making process during the provision of CMM services. Using grounded theory, we devised a theoretical proposition, which derived from narratives of 11 pharmacists, observations of CMM consultations and clinical case discussions. The results suggested that understanding the patient’s medication experiences can guide the professional to identify and resolve drug therapy problems. According to the participants, the medication experience can lead the practitioner to two courses of action: to improve health literacy, helping the patient overcome barriers to medication use; or to adapt the intervention, matching the pharmacotherapy to the patient’s routine. This knowledge can be used as a guide to teach pharmacy students and novice pharmacists how to incorporate patients’ medication experiences into clinical decision-making.