Genus Allium (F. Amaryllidaceae) includes a wide variety of edible foods widely consumed for their nutritive as well as health benefits. Seven Allium species, viz., chives, Egyptian leek, French leek, red garlic, white garlic, red onion, and white onion aerial parts were assessed for metabolome heterogeneity targeting both aroma and nutrients phytochemicals. A headspace solid-phase microextraction (HS-SPME) and gas chromatography–mass spectrometry (GC–MS) were employed. Results revealed extensive variation in volatiles and nutrients profile among the seven Allium species represented by a total of 77 nutrients and 148 volatiles. Among edible Allium species, French leek encompassed high levels of nutrients, viz., sugars, fatty acids/esters, organic acids, and amino acids, compared to Egyptian leek. Sulfur aroma compounds appeared as the most discriminatory among Allium, taxa accounting for its distinct flavor. Furthermore, chemometric analysis of both datasets showed clear discrimination of the seven Allium species according to several key novel markers. This study provides the first comparative approach between edible and inedible aerial leafy parts of Allium species providing novel insight into their use as functional foods based on such holistic profiling.