ABSTRACT Integrating grain yield, component traits and metabolite profiles aids in selecting drought‐adapted and climate‐smart crop varieties preferred by end users. Understanding the trends and magnitude of grain‐based metabolites is vital for selecting wheat genotypes with higher grain yield, drought tolerance, water use efficiency and product profiles. The aim of this study was to determine the response of newly developed wheat genotypes for grain yield and component traits and metabolites under drought stress to guide selection. One hundred wheat genotypes were preliminarily evaluated for agro‐morphological traits and water use efficiency under drought‐stressed and non‐stressed conditions during the 2022 and 2023 growing seasons using a 5 × 20 alpha lattice design with two replications. Ten high‐yielding genotypes were selected based on grain yield and were validated for agronomic traits and water use efficiency (WUE), and grain samples were assayed to profile their key metabolites under drought‐stressed conditions. Significant differences existed ( p < 0.05) among the tested wheat genotypes for yield and yield components, WUE, drought tolerance and major metabolites to discern trait associations. The grain yield of the 10 genotypes ranged from 590.00 g m −2 (genotype LM70 × BW140) to 800.00 g m −2 (BW141 × LM71) under drought‐stressed treatment, whilst under non‐stressed it ranged from 760.06 g m −2 (LM70 × BW140) to 908.33 g m −2 (LM71 × BW162). Grain yield‐based water use efficiency of the assessed genotypes was higher under non‐stressed (0.18 g mm −1 ) than drought‐stressed (0.17 g mm −1 ) conditions. The highest drought tolerance index (211.67) and stress susceptibility index (0.77) were recorded for BW162 × LM71, whilst the lowest tolerance index (23.33) and stress susceptibility index (0.09) were recorded in BW141 × LM71. Grain metabolites, including the apigenin‐8‐C‐glucoside (log2Fold = 3.00) and malate (log2Fold = 3.60) were present in higher proportions in the high‐yielding genotypes (BW141 × LM71 and LM71 × BW162) under drought‐stressed conditions, whilst fructose (log2Fold = −0.50) and cellulose (log2Fold = −3.90) showed marked decline in the two genotypes. Based on phenotypic and metabolite profile analyses, genotypes BW141 × LM71 and LM71 × BW162 were selected for being drought‐tolerant, water‐use efficient and recommended for production or breeding. The findings revealed associations between yield components, water use efficiency and grain metabolites to guide the selection of best‐performing and drought‐tolerant wheat varieties.