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Background Preconception iron and folic acid supplementation (IFAS) is a key intervention to prevent neural tube defects (NTDs) and maternal and child iron deficiency anaemia (IDA). Despite its potential benefits, many healthcare systems rarely provide preconception IFAS to women who plan to become pregnant and mothers with a history of spontaneous abortion who declined contraceptive use. The aim of this study was to explore stakeholder perspectives on the challenges and opportunities for implementing preconception IFAS for these high-risk groups in the Ethiopian healthcare system, a country with a high burden of NTDs and IDA.Methods An exploratory qualitative study was conducted among 45 participants, including women attending antenatal care, women planning pregnancy including mothers with a history of spontaneous abortion who declined contraceptive use, healthcare providers and maternal and child care experts. Participants were selected using purposive sampling. Data were first analysed separately for each participant group and then triangulated to synthesise a comprehensive understanding of practices, challenges and opportunities.Results Major barriers operate at policy, health system and individual levels, including the absence of a structured national preconception care programme, inadequate health system capacity, limited knowledge among women and providers, behavioural constraints to preconception care utilisation and a high prevalence of unplanned pregnancies. However, existing health extension programme, family planning clinic and gynaecology department with supportive policy frameworks offer viable entry points for integrating preconception IFAS.Conclusion This study identified major gaps in the implementation of preconception IFAS within the Ethiopian healthcare system. Women with a history of spontaneous abortion who decline contraceptive use represent an overlooked group with unmet preconception nutritional needs. Strengthening policy, training and community awareness is essential. Future implementation research is needed to support integration of preconception IFAS and improve maternal and neonatal outcomes, contributing to Sustainable Development Goals for maternal and child health.