Pulses are well known to be gluten-free functional foods that provide a rich source of nutritional and healthy compounds with antioxidant-promoting activity. In the present study, the bioactive compounds, dietary fibre, arabinoxylans, individual phenolic compounds and tocopherols, were evaluated in different lentil flours (raw and extruded at 140 and 160 °C) formulated with nutritional yeasts, along with the changes induced by the extrusion process. The total dietary fibre and arabinoxylan content significantly (p < 0.05) increased after the extrusion process while a significant decrease of all tocopherol isoforms was also observed. Catechin, caffeic, kaempferol and quercetin derivatives were identified in the raw and extruded lentil flours. The decreases of total phenolic and individual phenolic compounds were directly related to the extrusion temperature; total phenolics and catechin hexoside exhibited a larger decrease in the lentil flours formulated with higher content of nutritional yeast (12 and 16%). The antioxidant activity results, determined using different assays, reflected the important effect of extrusion processing and food ingredients.