Chia (Salvia hispanica L.), a rich plant-based source of omega-3 fatty acids, is being explored as a climate-resilient alternative crop in India. However, limited genetic variability and the absence of high-yielding cultivars constrain its wider adoption. To address this, a mutation breeding program was initiated using gamma irradiation (400, 500, and 600 Gy) on seeds of two varieties: white-seeded ‘Champion’ and black-seeded ‘Black selection-1’. The M₁ generation evaluation showed that increasing radiation doses led to reduced germination, delayed emergence, and suppressed seedling vigour, particularly in the black-seeded variety. Germination in Champion decreased from 88.50% (0 Gy) to 57.75% (600 Gy), and it decreased from 86.25% to 56.50% in Black selection-1. Successive mutant generations (M₂–M₆) revealed novel phenotypes, including bold seeds, pigmentation changes, crinkled foliage, altered spike architecture, and early flowering. Importantly, several M₆ lines exhibited a superior agronomic performance. Mutant line 94-1-1 recorded the highest yield of 2.46 kg/plot (1094.81 kg/ha), which represented an 80.68% increase over Champion (605.93 kg/ha) and 28.52% over Black selection-1 (851.85 kg/ha), with earlier maturity (104 days vs. 117 and 115 days). Other high-performing lines, such as 94-3-3 and 94-3-1, also showed yield improvements ranging from 65% to 70% over Champion, coupled with moderately reduced maturity durations (111–113 days). These findings highlight the effectiveness of gamma irradiation for inducing stable genetic variability and developing high-yielding, early-maturing varieties. This study underscores the potential of mutation breeding to develop superior Chia cultivars suited to Indian dryland and climate-vulnerable regions.