Missed opportunities for vaccination (MOVs), estimated to be about 32-47% of child healthcare clinic visits in various settings globally, contribute to unfulfilled childhood vaccination coverage targets in the African region. We assessed the extent of MOVs, identify local drivers and test interventions to reduce MOVs in Malawi. We conducted in-depth and key informant interviews with administrators of district hospitals and officers in charge of community health facilities. Focus group discussions were held with health workers and caregivers of children under 24 months of age who received services from study health facilities in Malawi. Coverage rates were collected from the health facility records. Vaccination is appreciated in the communities, but coverage is generally below targets. In some facilities, reported coverage was less than 50%. Opportunities to provide up-to-date vaccination for children were missed due to lack of awareness and knowledge of health workers and caregivers, attitude and priority of health workers, long waiting time, poor coordination and referral of eligible children by clinicians and nurses and overall lack of a team approach to vaccination perceived as a responsibility of health surveillance assistants. Other notable issues included limited time of caregivers labouring on estate farms, unavailability of vaccines resulting from poorly functioning of cold chain equipment and limited transport and failure to appreciate the impact of MOV on poor immunization coverage. Simple, low-cost, pragmatic and community-driven interventions that may reduce MOVs and improve vaccine coverage.