The electronic health record (EHR) and patient portal are used increasingly for clinical research, including patient portal recruitment messaging (PPRM). Use of PPRM has grown rapidly; however, best practices are still developing. In this study, we examined the use of PPRM at our institution and conducted qualitative interviews among study teams and patients to understand experiences and preferences for PPRM. We identified study teams that sent PPRMs and patients that received PPRMs in a 60-day period. We characterized these studies and patients, in addition to the patients' interactions with the PPRMs (e.g., viewed, responded). From these groups, we recruited study team members and patients for semi-structured interviews. A pragmatic qualitative inquiry framework was used by interviewers. Interviews were audio-recorded and analyzed using a rapid qualitative analysis exploratory approach. Across ten studies, 35,037 PPRMs were sent, 33% were viewed, and 17% were responded to. Interaction rates varied across demographic groups. Six study team members completed interviews and described PPRM as an efficient and helpful recruitment method. Twenty-eight patients completed interviews. They were supportive of receiving PPRMs, particularly when the PPRM was relevant to their health. Patients indicated that providing more information in the PPRM would be helpful, in addition to options to set personalized preferences. PPRM is an efficient recruitment method for study teams and is acceptable to patients. Engagement with PPRMs varies across demographic groups, which should be considered during recruitment planning. Additional research is needed to evaluate and implement recommended changes by study teams and patients.