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Roasted citron watermelon seeds are eaten as snacks based on maturity indices. Association between coat colour, nutrient composition and physical properties is unknown. Therefore, seed coat thickness (SCT), hardness and popping yield (PY) may influence roasting quality and chewability. Understanding seed nutrient composition, physical properties, and coat colour associations allows selection for desirable traits. Forty accessions were analysed for mineral elements using flame atomic emission spectrometry (FAES) for K and flame atomic absorption spectrometry (FAAS) for Mg, Cu, Mn, and Zn. Physical properties such as (seed thickness (ST), weight required to crack seed (WRCS), SCT, and PY were analysed. Data was subjected to correlation and Principal Component Analysis. Significant differences were observed for mineral elements and physical properties (P < 0.05). Dark and red seeds had high ST and SCT but low WRCS, Cu and Zn compared to brown seeds. Significantly lower PY and high Ca content were recorded for dark seeds. Dark seeds had high hemicellulose (19.58%), cellulose (39.17%) and lignin (30.08%). Popping yield was positively correlated with lightness (r = 0.72; P < 0.001) and negatively correlated with Ca (r = -0.77; P < 0.001). Seeds with lighter colours had higher popping yield and less Ca, implying that coat colour influences palatability, nutrient composition and physical properties. Study findings will guide breeding strategies to enhance the nutritive value of seeds. [Display omitted]. • Seed coat colour was defined technically by RGB colour model. • Nutrients were measured by fast sequential atomic absorption spectrometer. • Dark and red seeds were good sources of Cu and Zn. • Seed physical properties, nutrient composition and palatability, are associated with coat colour. • Brown and red coloured seeds have a higher popping yield than dark-coloured seeds. [ABSTRACT FROM AUTHOR]