Introduction: School-based immunization programs offer an accessible route to routine vaccines for students. During the COVID-19 pandemic, school closures to comply with public health measures had a drastic effect on school-based immunization program delivery and associated vaccine uptake. We sought to integrate findings from a mixed methods study to co-develop evidence-based and theory-informed recommendations with a diverse group of stakeholders (i.e., decision makers, healthcare providers, school staff, parents and adolescent students) to address barriers to new and existing school-based immunization programs. Methods: Findings from a mixed methods study were integrated using a joint display and narrative summary. These findings were mapped through the Behaviour Change Wheel, a series of tools designed to facilitate the development of behaviour change interventions. Draft recommendations were provided to previous mixed methods study participants who consented to participating in future phases of the research study (n = 26). Feedback was captured using a Likert-scale survey of acceptability, practicality, effectiveness, affordability, safety and equity (APEASE) criteria, with feedback and additional insights captured using open-ended textboxes. Data was used to revise and finalize recommendations. Results: Applying the Behaviour Change Wheel, we drafted 26 evidence-based, theory-informed recommendations to address barriers to school-based immunization programs. Participants (n = 16) provided feedback, with half of the recommendations scoring 80% or higher across all six APEASE criteria. The remaining 13 recommendations received a moderate score across one or more criteria. Stakeholders identified a high level of interest in expanding the use of e-consent forms, expanding programming to offer a meningitis B vaccine, and recommendations to ease student anxiety. Conclusion: We co-developed a range of recommendations to improve school-based immunization programs with stakeholders using data generated from a mixed methods study. Implementation of any single or combination of recommendations will need to be tailored to local clinic procedures, school system and health system resources.