Suspect and non-targeted screening approaches are a matter of increasing interest notably with regard to the Exposome contextual framework, but their application to human samples still remains limited at this date. The aim of the present study was to develop a non-targeted workflow from sample preparation to data processing and method assessment to characterise the human internal chemical exposure at early life stage. The method was focused on human milk to investigate mother and newborn exposure to known organic contaminants and to extend the characterisation to unknown compounds. We specifically focused on halogenated biomarkers of exposure due to persistence and potential toxicological impact reasons. The newly developed approach was based on a simple and fast sample preparation followed by a comprehensive analysis by both liquid and gas phase chromatography coupled to high resolution mass spectrometry. Critical steps of the non-targeted workflow as the method assessment have been addressed with a reference mix of 30 chlorinated and brominated contaminants encompassing various substances groups and a statistical approach. Data processing until the identification of biomarkers of exposure was possible with homemade bioinformatics tools. On the other hand, the method was validated by the identification of historical chemicals as hexachlorobenzene and p,p’-DDE and emerging chemical as 4-hydroxychlorothalonil. This approach opens the door to further extensions and consolidations to offer new capabilities for exposomics and environmental health research.