The aim of the present study was to evaluate the effect of both heat stress and simulated intramammary infection on milk metabolomics in dairy goats. Eight multiparous Murciano-Granadina dairy goats (2.2 ± 0.1 L/d; 100 ± 5 DIM, 42 ± 2 kg BW) were maintained under 2 environmental conditions varying in temperature, relative humidity (RH) and temperature-humidity index (THI): 1) 4 goats under thermoneutral (TN; 15 to 20°C, RH = 50 ± 5%, THI = 59 to 65), and 2) 4 goats under heat stress conditions (HS; 35°C from 0900 to 2100 and 28°C from 2100 to 0900, RH = 45 ± 5%, THI = 75 to 83). Adaptation of 11 d to the experimental treatments was allowed. On d 12, each animal had one udder half infused with 10 mg E. Coli lipopolysaccharide (LPS) and the other udder half as the control with 0.9% saline (CON). This resulted in 4 treatment combinations: TN-CON, TN-LPS, HS-CON, and HS-LPS. Milk samples (0, 4, 6, 12, and 24 h) were collected and analyzed by ¹H NMR spectroscopy operating at 600 MHz. Data were processed by the R program (pls package), in which the principal component analysis and partial least square–discriminant analysis were used to identify possible metabolite markers in milk. Citrate increased (log₂ fold change = 1.79; P = 0.010) in milk of HS goats. The increment in milk citrate might explain the known deteriorated coagulation properties during the cheese-making from the milk of heat-stressed animals. On the other hand, the LPS challenge resulted in an increment in milk acetone, β-hydroxybutyrate, alanine, choline, lactate, and isobutyrate. In conclusion, high ambient temperatures and udder inflammation dramatically affected the metabolomic profile of milk. Milk citrate and ketone bodies were detected as potential markers for heat stress and udder inflammation, respectively. Project AGL-2013-44061-R (Plan Nacional, MINECO, Spain).