Stir-frying, one of the most popular method to prepare Brassica vegetables in Indonesia, can retain the content of the alleged health promoting glucosinolates. Meanwhile, long-term steaming and fermentation considerably reduce the glucosinolate content. By analysing the mechanisms underlying glucosinolate changes during preparation, alternative procedures or conditions to enhance the retention of glucosinolates were proposed. For fermentation, prior inactivation of myrosinase enzyme resulted in a higher retention of glucosinolate. For steaming, a reduction of the steaming time was shown beneficial to have a higher glucosinolate content. A mathematical modelling approach was successfully applied to describe the effects of variation in the conditions and processes on the glucosinolate content of products and to optimise them in order to get a more optimal glucosinolate content in the prepared products. Besides improvement of the content of vegetable products, the present study also yields important information to make a more accurate estimation of the dietary intake of glucosinolates in prepared dishes. Such estimation is important for establishing the relation between intake of phytochemicals and health effects like reducing the risk of certain diseases.