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Background The COVID-19 pandemic resulted in extreme strain on health systems including the health workforce, essential health services and vaccination coverage. We examined disruptions to immunisation and maternal and child health (MCH) services, concerns of personal well-being and delivery of healthcare during the pandemic as well as factors associated with self-reported trauma or burnout among healthcare providers (HCPs).Methods In March–April 2022, we conducted a cross-sectional survey among HCPs in two provinces of Indonesia. HCPs involved in COVID-19 or routine immunisation and MCH services were randomly selected from district/city health office registration lists. We descriptively analysed service disruptions experienced by HCPs as well as trauma, burnout and concerns of personal well-being and delivery of healthcare during the pandemic. Multivariate logistic regression analyses were undertaken to identify factors associated with trauma or burnout.Results We recruited 604 HCPs. Mobilisation of staff from routine health services to COVID-19 response duties was a key reason for service disruptions (87.9%). Strategies such as community outreach and task shifting were implemented to overcome disruptions. Trauma or burnout during the pandemic was reported by 64.1% HCPs, with 23.5% reporting worse mental or emotional health.Factors associated with trauma or burnout included delivery of COVID-19 immunisation (adjusted OR (aOR) 2.54, 95% CI 1.08 to 5.94); and delivery of both COVID-19 immunisation and routine immunisation compared with no involvement in vaccination programmes (aOR 2.42, 95% CI 1.06 to 5.52); poor treatment in the workplace (aOR 2.26, 95% CI 1.51 to 3.38) and lower confidence to respond to patient queries on COVID-19 immunisation (aOR 1.51, 95% CI 1.03 to 2.22).Conclusion HCPs experienced service disruptions, trauma and burnout and implemented strategies to minimise disruptions to service delivery and improve patient experiences. Our study highlights the need to ensure that workforce resilience and strategies to protect and support HCPs are considered for pandemic planning, preparedness and management.