Background Seven housing and health services organizations were guided through a process of translating Chapter Six of the Canadian Guidelines for Recovery-Oriented Practice into a recovery-oriented innovation and plan for its implementation. At the time of the COVID-19 outbreak and lockdown measures, six of the seven organizations had begun implementing their chosen innovation (peer workers, wellness recovery action planning facilitator training, staff training and a family support group). This mid-implementation study used the Consolidated Framework for Implementation Research (CFIR) to identify contextual factors that influenced organizations to continue or postpone implementation of recovery-oriented innovations in the early months of the COVID-19 pandemic. Methods Twenty-seven semi-structured 45-min interviews were conducted between May and June 2020 (21 implementation team members and six providers of the innovation (trainers, facilitators, peer workers). Interview guides and analysis were based on the CFIR. Content analysis combined deductive and inductive approaches. Summaries of coded data were given ratings based on strength and valence of the construct’s impact on implementation. Ratings were visualized by mid-implementation outcome and recovery innovation to identify constructs which appear to distinguish between sites with a more or less favorable mid-implementation outcomes. Results Four mid-implementation outcomes were observed at this snapshot in time (from most to least positive): continued implementation with adaptation (one site), postponement with adaptation and estimated relaunch date (four sites), indefinite postponement with no decision on relaunch date (one site), and no implementation of innovation yet (one site). Two constructs had either a negative influence (external policies and incentives—renamed COVID-19-related external policy for this study) or a positive influence (leadership engagement), regardless of implementation outcome. Four factors appeared to distinguish between more or less positive mid-implementation outcome: adaptability, implementation climate and relative priority, available resources, and formally appointed internal implementation leaders (renamed “engaging implementation teams during the COVID-19 pandemic” for this study). Conclusions The COVID-19 pandemic is an unprecedented outer setting factor. Studies that use the CFIR at the mid-implementation stage are rare, as are studies focusing on the outer setting. Through robust qualitative analysis, we identify the key factors that shaped the course of implementation of recovery innovations over this turbulent time.