Despite the global interest to increase the world’s carbon stocks, most carbon sequestration strategies have largely depended on woody ecosystems whose production is threatened by the continuous shortage of land; hence, the need to explore viable alternatives. The potential of bananas to sequester carbon has been reported but there is limited knowledge on the performance of various cultivars especially in Uganda; perhaps due to lack of viable equations to estimate specific carbon stocks lost in global assessments. Therefore, this study aimed at exploring the variability in carbon stocks of East African Highland Banana (EAHB) cultivars grown in two districts of Uganda. Specifically, the study intended to: 1) Develop allometric relationships for biomass estimation of EAHB cultivars; 2) Determine their carbon content; and 3) Estimate their carbon stocks. Plant and soil data were collected using destructive and non-destructive techniques in 30×30m2 sampling plots for 4 cultivars (Kibuzi, Nakitembe, Enyeru and Nakinyika) in two districts: Mbarara and Lwengo. Results show that biomass differed across cultivars (P<0.001); hence four equations (Enyeru, Nakinyika, Kibuzi_Nakitembe and Generic) were developed following an exponential function, y=Aexp(ax), using Diameter at breast height as the predictor variable with an R 2 range of 82-94%. EAHB mean carbon content varied significantly with growth stage (P<0.05) (47.6% for maiden plants before flowering and 48.8% for mature plants with a developed bunch). Total carbon and SOC stocks did not differ considerably across cultivars (P>0.05). Plant carbon stock differed (P<0.05) with the lowest recorded in Nakinyika (0.37±0.19 Mgha-1) and Nakitembe in Mbarara (0.40±0.19Mgha-1), and highest in Enyeru (1.64±0.18 Mgha-1). The proportion of banana to SOC stock was very small across cultivars (0.4-2%).