Germination is an efficient and natural strategy that allows the modification of the nutritional value and the nutraceutical properties of seeds, enabling one to tailor the process according to its final use. This study aimed at optimization of germination conditions to produce novel lentil flours with improved nutritional and functional features. Response Surface Methodology (RSM) was applied to model the effect of temperature (15–27 °C) and time (1–5 days) on different nutritional and quality parameters of lentil flours including proximate composition, content and profile of fatty acids, content of phytic acid, ascorbic acid and γ‐aminobutyric acid (GABA), content and profile of phenolic compounds, antioxidant activity, expected glycemic index (GI) and color during germination. As shown by RSM polynomial models, sprouting promoted the reduction of phytic acid content and enhanced the levels of ascorbic acid, GABA, insoluble phenolic compounds, anti-oxidant activity and expected GI, and modified the color of the resultant lentil flours. RSM optimization of germination temperature and time using desirability function revealed that the optimal process conditions to maximize the nutritional, bioactive and quality properties of sprouted lentil flours were 21 °C for 3.5 days.