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Background Informed decision aids provide information in the context of the patient's values and improve informed decision making (IDM). To overcome barriers that interfere with IDM, our team developed an innovative iPad-based application (aka “app”) to help patients make informed decisions about colorectal cancer screening. The app assesses patients' eligibility for screening, educates them about their options, and empowers them to request a test via the interactive decision aid. Objective The aim of the study is to explore how informed decision aids can be implemented successfully in primary care clinics, including the facilitators and barriers to implementation; strategies for minimizing barriers; adequacy of draft training materials; and any additional support or training desired by clinics. Design This work deals with a multicenter qualitative study in rural and urban settings. Participants A total of 48 individuals participated including primary care practice managers, clinicians, nurses, and front desk staff. Approach Focus groups and semi-structured interviews, with data analysis were guided by thematic analysis. Key Results Salient emergent themes were time, workflow, patient age, literacy, and electronic health record (EHR) integration. Saving time was important to most participants. Patient flow was a concern for all clinic staff, and they expressed that any slowdown due to patients using the iPad module or perceived additional work to clinic staff would make staff less motivated to use the program. Participants voiced concern about older patients being unwilling or unable to utilize the iPad and patients with low literacy ability being able to read or comprehend the information. Conclusion Integrating new IDM apps into the current clinic workflow with minimal disruptions would increase the probability of long-term adoption and ultimate sustainability. NIH trial registry number R01CA218416-A1.