Background The study investigated the essential oil composition, metal profile and physiochemical properties of Citrus macrophylla Wester fruits collected from Agricultural Research Corporation, Shambat area, Khartoum North, Sudan. The species was introduced by one of the authors Dr. Moawia E. Mohamed from the National Repository of Citrus and Dates of Riverside, California, USA. This species is known as universal rootstock. Results The graphite furnace–atomic absorption spectrometry determined the presence of sodium (6.38 ppm), potassium (701.93 ppm), calcium (371.28 ppm), magnesium (54.78 ppm), cadmium (0.013 ppm), zinc (0.256 ppm) and lead (0.200 ppm). The content of peel, moisture and ash of C. macrophylla was measured as 18.35%, 23.75% and 2.04%, respectively. Among thirty compounds identified using gas chromatography–mass spectrometry, limonene is the major compound (72.85%). The vitamin C (ascorbic acid) content of C. macrophylla juice was determined as 55.0 mg/100 g. The fruit diameter, fruit weight and percentages of juice, peel and seed were determined as 91.4 mm, 276.5 g, 47.92%, 26.37% and 19.20%, respectively. The pH value, total soluble solids (TSS), titratable acidity (TA) and ripening index (RI) of C. macrophylla are found to be 3.50, 8.00%, 7.44% and 10.81, respectively. Conclusion The results in this study suggested that C. macrophylla could be beneficial in food as healthy juice.