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This study explores the potential of seeds from fruit and vegetable processing waste as feedstocks for biodiesel biocomponent production. Fatty acid methyl esters (FAMEs), obtained through a transesterification reaction, were extracted using ultrasound-assisted extraction and identified by gas chromatography–mass spectrometry (GC–MS) in selected ion monitoring (SIM) mode. A total of 31 to 34 individual FAME compounds were identified across all samples. The fatty acid profiles varied both quantitatively and qualitatively depending on the raw material; however, unsaturated FAMEs predominated over saturated ones in all cases. The highest proportions were observed for γ-linolenic acid (C18:3n6), particularly in apple, melon, lemon, and pumpkin seeds. Substantial contributions of oleic acid (C18:1n9c) were found in apple, quince, cherry, and melon seeds, while linolelaidic acid (C18:2n6t) dominated in melon, pumpkin, quince, and cherry seeds. The highest total FAME contents were recorded for apple, melon, lemon, and pumpkin seeds, while the lowest values were observed in apricot and pepper seeds. Among the materials studied, grape seeds proved to be the most promising feedstock, exhibiting a favorable cetane number and a beneficial fatty acid profile characterized by high monounsaturated fatty acid (MUFA) content, low polyunsaturated fatty acid (PUFA) content, and a moderate fraction of saturated fatty acids (SFAs). Plum and peach seeds also showed significant potential, but their higher PUFA levels may compromise oxidative stability and could require antioxidant supplementation or blending with MUFA-rich feedstocks.