The aim of the study was to investigate how the extrusion of faba bean seeds (var. Albus) and/or the addition of protease to pigs’ diets affected the animals’ growth parameters, digestibility of nutrients, selected physiological parameters of the digestive tract, and biochemical blood parameters. A 28-day experiment was conducted on 32 pigs weighing 9 ± 0.2 kg. The animals were allocated to four treatments in a 2 × 2 factorial arrangement with the main effects of extrusion (raw or extruded) and effects of protease supplementation (0 and 0.05%). Extrusion reduced the levels of neutral detergent fibre, trypsin inhibitor, phytate-P, and resistant starch but did not improve the digestibility of protein and dry matter in faba bean seeds. The pigs’ growth performance, ileal digestibility, enzyme activity, and morphometric parameters of the ileum were not significantly affected by extrusion, except for a higher feed intake between the 15th and 28th day of the experiment. The protease supplementation gave comparable results as the diet without protease, except the feed conversion ratio (in the periods of 15–28th day and 0–28th day), which was higher than in the groups without protease. The extrusion and protease increased acetate and acetoacetate contents in the cecal digesta, but propionate, butyrate, and isovalerate concentrations in the digesta of the pigs in this group were lower. Thanks to protease supplementation, protein and oil levels in the diet were reduced, which cut the cost of feed mixtures. The extrusion and protease additive combined together did not improve the pigs’ growth performance in this experiment.