Bovine mastitis is one of the most common diseases in dairy cows, and it causes significant economic losses in dairy industries worldwide. Gram-positive and Gram-negative bacteria can cause bovine mastitis, and many of them have developed antimicrobial resistance. There is an urgent need for novel therapeutic options to treat the disease. Larrea tridentata-derived compounds represent an important potential alternative treatment. The aim of the present study was to isolate and characterize antibacterial compounds from Larrea tridentata against multidrug-resistant bacteria associated with bovine mastitis. The L. tridentata hydroalcoholic extract (LTHE) exhibited antibacterial activity. The extract was subjected to a bipartition, giving an aqueous fraction (moderate antibacterial activity) and an organic fraction (higher antibacterial activity). Chromatographic separation of the organic fraction enabled us to obtain four active sub-fractions. Chemical analyses through HPLC techniques were conducted for the LTHE, fractions, and sub-fraction Ltc1-F3, from which we isolated two compounds, characterized by 1H and 13C NMR analyses. Compound nor-3 demethoxyisoguaiacin exhibited the best antibacterial activity against the evaluated bacteria (MIC: 0.01–3.12 mg/mL; MBC: 0.02–3.12 mg/mL). The results indicated that nor-3 demethoxyisoguaiacin can be used as an alternative treatment for multidrug-resistant bacteria associated with mastitis.