Germination is a rising technique that improves the nutritional, technological, and functional quality of legume flours, making them a modified ingredient with potential benefits to human health and varied food applications (Huang, Cai, & Xu, 2017). There is a strong industrial interest to incorporate legumes to food development due to its high protein content, low cost of production and lower impact to environmental pollution. Aims of sustainable development can be implanted through innovation in plant-based foods. Grains from Lupinus angustifolius are a potential source of vegetable protein. It has been reported that lupin germination increases the content of phenolic compounds, tocopherols, and vitamins C and E, improving the antioxidant capacity (Kamran, Phillips, Harman, & Reddy, 2023). On the other hand, grains germination leads to changes in the composition of isoflavonoids, compounds that take part in the prevention of several chronic degenerative diseases (Aisyah, Vincken, Andini, Mardiah, & Gruppen, 2016). It has been reported that the germination of Lupinus angustifolius increases the functional properties as water and oil absorption, foaming capacity, and emulsification (Muñoz-Llandes et al., 2022), which favor its use in foods. However, the nutritional and structural properties of raw materials can be modified during processing. Temperature is likely a major factor that alters nutrient bioavailability during cooking. In processes as extrusion cooking, where high temperatures are used, there are reports of modifications in carbohydrates as starch, formation of amylose-lipid complexes, and degradation of compounds as vitamins and pigments (Gulati, Weier, Santra, Subbiah, & Rose, 2016). Proteins are denatured while trypsin inhibitors (non-nutritional compounds) are reduced or inactivated (Orozco-Angelino, Espinosa-Ramírez, & Serna-Saldívar, 2023). These alterations affect protein digestibility after extrusion (Nadeesha Dilrukshi, Torrico, Brennan, & Brennan, 2022). It has been reported that biological actions, such as antioxidant, immunoregulatory, antihypertensive, α-amylase inhibitory, and anti-inflammatory activities from protein of grains like barley, soy, beans, and amaranth increase after extrusion cooking (Montoya-Rodríguez, de Mejía, Dia, Reyes-Moreno, & Milán-Carrillo, 2014; Sharma, Gujral, & Singh, 2012; Sun, 2011; Yao & Ren, 2014). Gao et al. (2020) identified peptides from digested lupinus-based extrudates capable of inhibiting proinflammatory mediators as interleukin-6 (IL-6), tumor necrosis factor-α (TNF-α), and monocyte chemoattractant protein-1 (MCP-1) in RAW 264.7 macrophages induced with lipopolysaccharide (LPS). Paucar-Menacho et al. (2022) reported that the use of germinated wheat flours for 3 days increases the sensory attributes in extrudates, a brown color is generated and its acceptability increases. Similarly, a reduction in the hardness of the final product has been evidenced due to the use of sprouts that have undergone hydrolysis of macromolecules by enzymatic action during germination. The combination of knowledge about the multiple benefits associated with both the germination and the extrusion of food ingredients opens the panorama to a new approach: the use of sprouted grain flours in the preparation of extruded snacks. Although there is abundant information about the advantages that each of these processes can provide individually, the work that has been reported on the synergy of both processes to create value-added products is limited. The combination of germination and extrusion represents an alternative, allowing to maximize the benefits of the grains. The need to carry out additional research becomes evident, with the aim of supporting and demonstrating the advantages of including sprouts in the generation of extrudates. This is based on the molecular transformation that occurs during germination, which causes greater availability and functionality of proteins, as well as the release of simple sugars and the reduction of anti-nutritional compounds. Therefore, the aim of this research was to determine the optimum extrusion cooking conditions using ungerminated Lupinus angustifolius flour, to obtain a puffed extrudate, after to replicate the process with germinated flours at different times, and characterize the physicochemical and nutritional properties of the products obtained, evidencing the influence of the use of sprouted flours. In addition, it was sought to establish molecular changes and transformations through Fourier-transform infrared spectroscopy (FT-IR) and scanning electron microscopy (SEM).