BackgroundIn Nigeria, COVID-19 vaccines were delivered through outreach activities, as well as integrated within routine immunisation. However, evaluations of integrated approaches for novel vaccines are scarce. We aimed to understand the perceived benefits and challenges of integrating the COVID-19 vaccine within routine immunisation in Nigeria, and identify ways to strengthen this approach.MethodsWe conducted 30 semi-structured interviews with community members and healthcare workers in primary healthcare facilities (PHCs) in Jigawa (n = 16) and Oyo (n = 14) states, Nigeria from 08 August to 13 September 2022. Participants were selected purposively from PHCs. We obtained information on participants’ perception about routine immunisation, and perceived benefits and challenges associated with integrated COVID-19 vaccine delivery. Healthcare worker and community interviews were analysed separately following a thematic analysis approach.ResultsWe identified four themes that describe the community and healthcare workers’ responses, perceived impact, and the health system adaptions to the challenges associated with the integrated vaccine delivery approach. Community members expressed concern that children might be given COVID-19 vaccines instead of routine immunisations, while others appreciated the integrated approach due to their trust in the efficacy of COVID-19 vaccines, government, and healthcare providers. Healthcare providers perceived the integrated approach as improving vaccination coverage and awareness but noted additional problems of increased workload, vaccine scarcity, and prolonged clinic visits. Insufficient resources were subsisting barriers to effective integration in both states, but the provider’s gender was also a challenge in Jigawa state. Additionally, the use of incentives to generate demand had ambiguous effects in Jigawa state.ConclusionTaking an integrated approach to deliver COVID-19 vaccines was acceptable by healthcare providers but community members expressed concerns. Given existing vaccination programmes have persistent challenges, it is pertinent to address these barriers to enhance effectiveness of an integrated approach.