Context Crop production in Eastern Himalaya is constrained by combined effects of soil acidity and moisture deficit during post monsoon under a changing climate. Aim This study aimed to identify potential buckwheat genotypes and stress mechanisms in hill environments of Meghalaya (India). Method Field and microcosm experiments were conducted to study field performance, genotypic variability and physio-morphological efficiency in buckwheat. Key results Substantial genetic variability for shoot length (30.3–110 cm), crop canopy distribution (3.0–7.5 number of primary branches), leaf area retention (15.7–60.2 cm2/two leaves), 1000 seed weight (16.2–34.7 g) and seed yield (0.088–1.31 metric tonne (MT)/ha) was observed. Mean grain yield of buckwheat genotypes was 0.446 MT/ha whereas IC13411, IC24298 and IC37305 produced significantly higher seed yield (1.31, 1.28 and 1.14 MT/ha, respectively) accounting to 1.93, 1.87 and 1.67 times higher than average yield (0.680 MT/ha). Genotypes like IC42416, EC323730 and EC218784 have lower crop yields (0.8, 1.02, 0.93 MT/ha respectively). Interestingly, few high yielders (IC13411 and IC24298) exhibited higher photosynthetic rate (46.1 and 32.3 μmol/m2.s), increased stomatal conductance (311.0 and 326.2 mmol/m2.s), leaf chlorophyll (2.47 and 2.55 mg/g fresh weight (FW)) and carotenoids (95 and 106.3 μg/g FW). Chlorophyll a and b ratio (3.3 and 3.0) and total chlorophyll to carotenoids (4.2 and 4.0) were higher in high yielders (IC13411 and IC24298) compared to other low yielders. Conclusions Robust root systems, stomatal structure and higher cuticle wax ideally enhanced water use efficiency (WUE) and drought tolerance in high-yielding buckwheat genotypes. Implications IC13411 and IC24298 are promising for enhanced productivity in the mountainous ecosystem of Meghalaya.