Background Good nutrition and healthy growth during the first 1000days have lasting benefit throughout life. For this, equally important is the structural readiness of health facilities. However, structural readiness and nutrition services provision during the first 1000 days in Ethiopia is not well understood. The present study was part of a broader implementation research aimed at developing model nutrition districts by implementing evidence based, high impact and cost-effective package of nutrition interventions through the continuum of care. This study was aimed at assessing structural readiness of health facilities and the extent of nutrition service provision in the implementation districts. Methods This assessment was conducted in four districts of Ethiopia. We used mixed method; a quantitative study followed by qualitative exploration. The quantitative part of the study addressed two-dimensions, structural readiness and process of nutrition service delivery. The first dimension assessed attributes of context in which care is delivered by observing availability of essential logistics. The second dimension assessed the service provision through direct observation of care at different units of health facilities. For these dimensions, we conducted a total of 380 observations in 23 health centers and 33 health posts. The observations were conducted at the Integrated Management of Neonatal and Childhood Illnesses unit, immunization unit, Antenatal care unit and Postnatal care unit. The qualitative part included a total of 60 key informant interviews with key stakeholders and service providers. Result We assessed structural readiness of 56 health facilities. Both quantitative and qualitative findings revealed poor structural readiness and gap in nutrition services provision. Health facilities lack essential logistics which was found to be more prominent at health posts compared to health centers. The process evaluation showed a critical missed opportunity for anthropometric assessment and preventive nutrition counselling at different contact points. This was particularly prominent at immunization unit (where only 16.4% of children had their weight measured and only 16.2% of mothers with children under six month of age were counselled about exclusive breastfeeding). Although 90.4% of pregnant women who came for antenatal care were prescribed iron and folic acid supplementation, only 57.7% were counselled about the benefit and 42.4% were counselled about the side effect. The qualitative findings showed major service provision bottlenecks including non-functionality of the existing district nutrition coordination body and technical committees, training gaps, staff shortage, high staff turnover resulting in work related burden, fatigue and poor motivation among service providers. Conclusion We found a considerable poor structural readiness and gaps in delivering integrated nutrition services with a significant missed opportunity in nutrition screening and counselling. Ensuring availability of logistics and improving access to training might improve delivery of nutrition services. In addition, ensuring adequate human resource might reduce missed opportunity and enable providers to provide a thorough preventive counselling service.