In this work, the antioxidant properties of methanolic extract of Larrea tridentata were assessed through the free radical scavenging method, ferric reducing antioxidant power and oxygen radical absorbance capacity. The phenolic acids content in the extract was quantified by high-performance liquid chromatography (HPLC) and the total phenol content by the Folin–Ciocalteu method. The extract was used as an antioxidant in biodiesel from canola oil composed mostly by fatty acid methyl esters identified and quantified by gas chromatography-mass spectrophotometry (GC-MS). The performance of the extract as an antioxidant was assessed by the oxidative stability index (OSI) with a Rancimat equipment at 100, 110, 120 and 130 °C. Additionally, the change of the peroxide value (PV) and the higher heating value under conditions of oxidative stress at 100 °C and air injection were measured. The antioxidant capacity of the extract reached 50,000 TAEC (micromole of Trolox antioxidant equivalent capacity per gram). The biodiesel was constituted by more than 70% of unsaturated fatty acid methyl esters (FAME), mainly methyl oleate. The time needed to reach a PV of 100 meqO2/kg was almost four times longer with an antioxidant concentration of 250 mg/L than the blank. The biodiesel showed an OSI time of 1.25 h at 110 °C, while it increased to 8.8, 15.89 and 32.27 h with the antioxidant at concentrations of 250, 500 and 1000 mg/L, respectively. The methanolic Larrea tridentata extract proved to have an antioxidant capacity and it is a green antioxidant in biodiesel to increase its oxidative stability. According to the results obtained, the L. tridentata methanolic extract is an alternative to the commercial synthetic antioxidants used in biodiesel nowadays.