Pulses are the seeds of legumes that are used for human consumption and include peas, beans, lentils, chickpeas, and faba beans. The bioactivity of pulse metabolites, including isoflavones and saponins, has been the subject of considerable research. However, there has been less consideration regarding the effect of cooking on these potentially beneficial phytochemicals. In this study the changes in concentration of isoflavones and saponins in 13 varieties of pulse including field pea, chickpea, and lentil is studied in whole seed, hydrated seed, and cooked seed. It was found that the concentration of isoflavones studied (genistein, daidzein, formononetin, and biochanin A) was highest in chickpeas, that soaking altered the amount of isoflavones, and that cooking eliminated these isoflavones. By contrast the saponin content of the pulses was more varied and less effect of cooking was observed. This has implications for any dietary recommendation for these pulse varieties with respect to these micro-nutrients.