Lentil (Lens culinaris) is a high-protein crop with a promising potential as a plant-based protein source for human nutrition. This study investigated nutritional and anti-nutritional properties of whole seed lentil flour (LF) compared to lentil protein isolates (LPIs) prepared in pilot-scale by isoelectric precipitation (LPI–IEP) and ultrafiltration (LPI–UF). Fermentable oligosaccharides, disaccharides, monosaccharides, and polyols (FODMAPs) profiles showed significant reductions in total galacto-oligosaccharides (GOS) contents by 58% and 91% in LPI–IEP and LPI–UF, respectively, compared to LF. Trypsin inhibitor activity (TIA) levels based on dry protein mass were lowered by 81% in LPI–IEP and 87% in LPI–UF relative to LF. Depending on the stage of digestion, the in vitro protein digestibility (IVPD) of LPIs was improved by 35–53% compared to LF, with both products showing a similar long-term protein digestibility to that of bovine serum albumin (BSA). This work supports the use of purified LPI products as a novel source of high quality protein for food applications.