Pasture-based systems have advantages compared to confined systems, such as a higher proportion of beneficial milk fatty acids for their consumers. However, in mixed systems (grazing + total mixed ration), cows are more exposed to external climatic conditions. Due to climate change (high temperature or heavy rains), cows spend more time in confinement facilities where supplementation is offered, mainly in intensive mixed systems (high stocking rate). Therefore, the conditions of the facility during their confinement acquire great importance. To our knowledge, no studies have evaluated how the different facility conditions during confinement in a mixed system affect the fatty acid profiles in milk and cheese. The objective of this study was to compare the fatty acid profiles between mixed systems with different conditions during confinement (compost-bedded pack barns vs. outdoor soil-bedded pen) and mixed systems and confinement systems (100% total mixed ration) in a compost-bedded pack barns. In conclusion, the compost-bedded pack barns during confinement in a mixed system ensued a better milk quality (a higher percentage of Omega 3 (n-3) and C18:3 in the milk) compared to the outdoor soil-bedded pen. However, the fatty acid profiles in the milk, pooled milk (MilkP), and cheese were affected to a greater extent by the feeding management than by controlling the environment during the confinement.