Jujube (Ziziphus mauritiana L.) holds untapped potential for morphological and biochemical diversity, yet their adaptation and performance under medium lowland agroecosystems remain underexplored. This study aimed to evaluate the genetic diversity, morphological traits, yield-related traits, and biochemical composition of 19 jujube genotypes to identify superior genotypes suitable for medium lowland conditions, typically utilised for irrigated rice cultivation in Cumilla, Bangladesh. The research was conducted over two consecutive growing seasons (2022-2023 and 2023-2024) and focused on assessing yield and biochemical components to determine overall genotype performance and adaptability. Genetic parameters such as the genetic coefficient of variation (GCV), phenotypic coefficient of variation (PCV), heritability, genetic advance (GA), and genetic advance as a percentage of the mean (GA%) were analysed to quantify trait variability and selection potential. Notably, fruit length, fruit width, fruit weight, pulp weight, and vitamin C concentration exhibited high heritability and substantial GA, indicating their potential for genetic improvement. Correlation analyses revealed significant relationships between morphological and biochemical traits, with fruit size and weight positively correlated with total soluble solids (TSSs) and soluble sugars, whereas a negative correlation was observed with non-reducing sugar. Furthermore, fruit weight, pulp weight, juice weight, and TSSs were identified as key determinants for selecting high-yielding genotypes. Multivariate analyses, including hierarchical clustering, cluster mean evaluation, principal component analysis biplots, and heatmaps were employed to identify genotype groupings and trait-specific contributions and obtain variability for superior genotype selection. Among the evaluated genotypes, Ball Sunduri and Local Kul-4 demonstrated high performance in both yield and biochemical composition, making them suitable for cultivation in medium lowland agroecosystems. This study provides a nuanced understanding of the relationship between genetic diversity and environmental factors, contributing to the optimisation of jujube cultivation in diverse agroecological settings. By demonstrating the feasibility of medium lowlands as an alternative agroecosystem for high-value jujube production, this research paves the way for innovative land-use strategies and climate-resilient agricultural practices.