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Abstract Background Medication prescribing and discontinuation processes are complex and involve the patient, numerous health care professionals, organizations, health information technology (IT). CancelRx is a health IT that automatically communicates medication discontinuations from the clinic electronic health record to the community pharmacy dispensing platform, theoretically improving communication. CancelRx was implemented across a Midwest academic health system in October 2017. The health system also operates 15 outpatient community pharmacies. Objective The goal of this qualitative study was to describe how both the clinic and community pharmacy work systems change and interact over time regarding medication discontinuations, before and after CancelRx implantation. Approach Medical Assistants (n = 9), Community Pharmacists (n = 12), and Pharmacy Administrators (n = 3), employed by the health system were interviewed across 3-time periods between 2017 and 2018— 3-months prior to CancelRx implementation, 3-months after CancelRx implementation, and 9-months after CancelRx implementation. Interviews were audio recorded, transcribed, and conducted a hybrid analysis with deductive content analysis following the Systems Engineering Initiative for Patient Safety (SEIPS) framework and inductive analysis to capture additional codes and themes. Key results CancelRx changed the medication discontinuation process at both clinics and community pharmacies. In the clinics, the workflows and medication discontinuation tasks changed over time while MA roles and clinic staff communication practices remained variable. In the pharmacy, CancelRx automated and streamlined how medication discontinuation messages were received and processed, but also increased workload for the pharmacists and introduced new errors. Conclusions This study utilizes a systems approach to assess disparate systems within a patient network. Future studies may consider health IT implications for systems that are not in the same health system as well as assessing the role of implementation decisions on health IT use and dissemination.