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It was hypothesized that differences in production system and muscle type may influence the formation of lipid oxidation products (LOP) as well as protein oxidation (protein carbonyl compounds, PCC) during in vitro gastrointestinal digestion of chicken meat. To test our hypothesis, we investigated the formation of LOP and PCC after heating and in vitro gastrointestinal digestion of conventional and organic chicken breast and thigh meat and Wooden Breast meat. Prior to the in vitro digestion, thigh and breast meat was minced and heated. Digests of organic thigh meat had significantly higher levels of all LOP measured compared to conventional thigh meat (between +37% and +173%). Lower levels of LOP were found in digests of breast meat regardless of production system and Wooden Breast phenotype. LOP levels were associated with variations in heme-Fe, polyunsaturated fatty acids, carnosine, anserine and α-tocopherol. PCC levels were significantly higher in thigh meat than in breast meat after heating (+43%) and digestion (+25%), irrespective of the production system. The cut-dependent differences in composition and susceptibility to oxidation during in vitro digestion between organic and conventional chicken meat in the present study warrant further research to allow a comprehensive assessment of the health implications.