Pouteria lucuma fruit is commonly used to prepare desserts, but it is also sold as pulp or flour. Then, huge amounts of its seeds are produced as agro-industrial waste, frequently eliminated. This study aims at analyzing the presence of all metabolites in Pouteria lucuma seed oil (LSO) by GC-MS and GC-FID. Several compounds were tentatively identified, such as fatty acids, fatty alcohols, carotenes, phytosterols and tocopherols from LSO. A representative result was the high amount of β-sitosterol with 851.49 ± 1.29 mg/100 g of LSO, followed by stigmasterol with 75.42 ± 1.02 mg/100 g. Fatty acids with the highest content were oleic acid (13.57 ± 1.50 g/100 g of LSO), 9E-octadecenoic acid (6.85 ± 1.15 g/100 g of LSO), palmitic acid (5.44 ± 1.18 g/100 g of LSO) and stearic acid (2.12 ± 1.03 g/100 g of LSO). Therefore, metabolites tentatively identified in Pouteria lucuma seed oil have been linked to healthy properties based on a high amount of β-sitosterol present. This evidence could determine this agro-industrial waste with having beneficial properties, thus providing great added value.