As a follow up of a previous experiment done in dairy goats (Love et al., 2016; ADSA Annual Meeting) to elucidate the response to an E. coli endotoxin (LPS) challenge, milk data by nuclear magnetic resonance (¹H-NMR) from Murciano-Granadina dairy does in mid-lactation (n = 8; 2.2 ± 0.1 L/d) and submitted to 12–12 h photoperiod and thermoneutral (TN; THI_NRC = 65–59; n = 4) or heat stress (HS; THI_NRC = 83–75; n = 4) conditions (day-night, respectively), were reprocessed. THI (thermohigrometric) values were calculated according to NRC (1971). On d-12 of experiment, TN and HS does were infused with 2 mL of LPS (10 μg) in one udder-half, at random, whereas the other udder-half was with saline. Milk samples were collected post-LPS challenge (h 0, 4, 6, 12 and 24) and analyzed by ¹H-NMR spectroscopy. Data analyses were done by R v.3.2.3 and included PCA (principal component analysis) and PLS-DA (partial least square-discriminant analysis) assessment, with cross validation leave-one-out, to detect milk biomarkers. Biomarkers were identified by cow’s milk data (Sundekilde et al., 2013). Milk citrate increased in HS does (R² = 0.96; Q² = 0.24) indicating a shift in macrophages mitochondrial function (i.e., transporting mitochondrial citrate to cytosol to produce inflammatory mediators such as PGE₂, ROS and NO). When HS does were challenged with LPS, there were dramatic increases of choline, N-acetylcarbohydrates (i.e., N-acetylactosamine and N-acetyglucosamine) and l-lactate, as well as, a strong decrease of lactose in milk (R² = 0.79; Q² = 0.49). Expected benefits of choline (mainly synthesized from Met) were the modulation of the immune function by mean the neurotransmitter acetylcholine and the protective role of N-acetylcarbohydrates against the adherence of pathogenic bacteria to the mammary epithelium. l-Lactate reflected the activation of the immune system by mitochondrial-oxidative shift to cytosolic (glycolytic) pathway. In conclusion, the metabolomic profile of goat’s milk was markedly affected by the environmental conditions and the udder health status. Milk biomarkers indicated the occurrence of inflammatory stages in the mammary gland under HS and LPS stressing conditions, being citrate and choline, respectively, the most affected metabolites. Supported by MINECO Spain (Projects AGL-2013-44061-R and RTA2015-0035-CO3-02.