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The large-scale conversion of forests to agriculture has caused biodiversity loss, climate change, and disrupted dietary fatty acid balances, with adverse public health effects. Wild edibles like pine nuts, especially Pinus cembroides, provide sustainable solutions by supporting ecosystems and offering economic value. However, variability in seed quality limits market potential, and lipidomic studies on P. cembroides remain sparse. This paper underscores the ecological, social, and nutritional value of P. cembroides while advocating for advanced research to enhance its use as a non-timber forest resource in Mexico’s communal areas. It explores various analytical techniques, such as nuclear magnetic resonances (NMR), chromatography coupled with mass spectrometry (HPLC-MS, GC-MS) and GC coupled with flame ionization detector (GC-FID), highlighting extraction methods like derivatization, purification, and thin-layer chromatography. Likewise, some considerations are addressed for the treatment of data obtained in the detection of fatty acids from bioformatics and the evaluation of the data through statistical methods and artificial intelligence and deep learning. These approaches aim to improve fatty acid profiling and seed quality assessments, fostering the species economic viability and supporting sustainable livelihoods in rural communities, encouraging researchers across the country to explore the fatty acid composition of different P. cembroides populations can drive valuable insights into its nutritional and ecological significance. Such efforts can enhance understanding of regional variations, promote sustainable use, and elevate the specie’s economic and scientific value.