To support the transition towards more sustainable and healthy diets, viable alternatives to foods of animal origin need to be identified. Many plant-based protein sources are currently marketed with claims of minimal environmental impact, but very limited consideration has been given to their protein quality and bioavailable mineral content considering the fact that animal-based foods are typically the primary source of both in Western diets. In this study, traditionally consumed soy foods (cooked soybeans, soymilk, tofu) from different Swiss soybean cultivars were nutritionally characterized and the in vitro digestibility of individual amino acids and total protein were assessed using an in vitro model based on the static INFOGEST protocol; the protein quality was evaluated using the in vitro digestible indispensable amino acid score (DIAAS). The results reveal an increase in total protein in vitro digestibility across the traditional soy food production value chain: 52.1–62.7% for cooked soybeans, 84.1–90.6% for soymilk, and 94.9–98.4% for tofu. Protein quality, determined using the recommended amino acid pattern for 0.5–3 years old, was “low” (no claim) for cooked soybeans (DIAAS < 60), while soymilk (DIAAS = 78–88) and tofu products (DIAAS = 79–91) were of similar “good” protein quality, with considerably higher DIAAS values than those of cooked soybeans (P < 0.001). The iron and zinc contents in soy foods were substantial, but high molar ratios of phytic acid (PA) to iron (PA/Fe; >8) and PA to zinc (PA/Zn; >15) indicate a possible strong inhibition of iron and zinc bioavailability. Based on the DIAAS results, soymilk and tofu would be suitable plant-based alternatives to animal-based foods, while future efforts should focus on optimizing soybean preparation to overcome the negative effects of the plant tissue matrix as well as processing steps to reduce mineral absorption inhibiting substances.