Novel snack-type functional foods based on extruded lentil flours could convey the related health benefit of their bioactive compounds, provide a gluten-free alternative to consumers, and potentially increase the consumption of pulses. Extrusion treatment promoted an increase in galactopinitol, ciceritol, raffinose, stachyose and total α-galactoside content, in most lentil flours. As α-galactosides may act as prebiotics, they could convey beneficial effects to human and monogastric animals. Conversely, extrusion significantly (p < 0.05) reduced the inositol hexaphosphate content to less phosphorylated phytates (inositol pentaphosphate and inositol tetraphosphate), which provide health effects. The gluten-free formulation (control formulation #3) presented the highest significant (p < 0.05) drop in the inositol hexaphosphate of 14.7-fold decrease, but had a large increase in inositol pentaphosphate, due to extrusion processing. These two results are desirable in the finished product. Extrusion also caused a significant (p < 0.05) reduction in the trypsin content and completely inactivated lectin, in all processed samples.