Pulses display nutritional benefits and are recommended in sustainable diets. Indeed, they are rich in proteins and fibers, and can contain variable amounts of micronutrients. However, pulses also contain bioactive compounds such as phytates, saponins, or polyphenols/tannins that can exhibit ambivalent nutritional properties depending on their amount in the diet. We characterized the nutritional composition and bioactive compound content of five types of prepared pulses frequently consumed in France (kidney beans, white beans, chickpeas, brown and green lentils, flageolets), and specifically compared the effects of household cooking vs. canning on the composition of pulses that can be consumed one way or the other. The contents in macro-, micronutrients, and bioactive compounds highly varied from one pulse to another (i.e., 6.9 to 9.7 g/100 g of cooked product for proteins, 4.6 to 818.9 µg/100 g for lutein or 15.0 to 284.3 mg/100 g for polyphenols). The preparation method was a key factor governing pulse final nutritional composition in hydrophilic compounds, depending on pulse species. Canning led to a greater decrease in proteins, total dietary fibers, magnesium or phytate contents compared to household cooking (i.e., −30%, −44%, −33% and −38%, p < 0.05, respectively, in kidney beans). As canned pulses are easy to use for consumers, additional research is needed to improve their transformation process to further optimize their nutritional quality.