Abstract Background Within-consultation recruitment to primary care trials is challenging. Ensuring procedures are efficient and self-explanatory is the key to optimising recruitment. Trial recruitment software that integrates with the electronic health record to support and partially automate procedures is becoming more common. If it works well, such software can support greater participation and more efficient trial designs. An innovative electronic trial recruitment and outcomes software was designed to support recruitment to the Runny Ear randomised controlled trial, comparing topical, oral and delayed antibiotic treatment for acute otitis media with discharge in children. A qualitative evaluation investigated the views and experiences of primary care staff using this trial software. Methods Staff were purposively sampled in relation to site, role and whether the practice successfully recruited patients. In-depth interviews were conducted using a flexible topic guide, audio recorded and transcribed. Data were analysed thematically. Results Sixteen staff were interviewed, including GPs, practice managers, information technology (IT) leads and research staff. GPs wanted trial software that automatically captures patient data. However, the experience of getting the software to work within the limited and complex IT infrastructure of primary care was frustrating and time consuming. Installation was reliant on practice level IT expertise, which varied between practices. Although most had external IT support, this rarely included supported for research IT. Arrangements for approving new software varied across practices and often, but not always, required authorisation from Clinical Commissioning Groups. Conclusions Primary care IT systems are not solely under the control of individual practices or CCGs or the National Health Service. Rather they are part of a complex system that spans all three and is influenced by semi-autonomous stakeholders operating at different levels. This led to time consuming and sometimes insurmountable barriers to installation at the practice level. These need to be addressed if software supporting efficient research in primary care is to become a reality.