The effect of different processing techniques was studied on in vitro iron availability and phytate hydrolysis in high and low saponin content quinoa (Chenopodium quinoa, Willd) seeds. Water slurries of ungerminated and germinated quinoa flour were processed by cooking, soaking, and fermentation using Lactobacillus plantarum as starter. Iron solubility under physiological conditions (in vitro) was measured and used as an estimation of iron availability. Phytate (inositol hexaphosphate/IP6) and its degradation products were analysed by an HPLC method. The IP6 + IP5 content was reduced by cooking with 4 to 8%, germination with 35 to 39%, soaking with 61 to 76% and by fermentation with 82 to 98%. The highest reduction, about 98%, was obtained after fermentation of the germinated flour. Cooking had no effect on the amount of soluble iron. Iron solubility increased, however, two to four times after soaking and germination, three to five times after fermentation and five to eight times after fermentation of the germinated flour samples and was highly correlated to the reduction of IP6 + IP5 (P < 0.001). There was no difference between the quinoa varieties with regard to phytate reduction and iron solubility. The pH in fermented samples was reduced from 6.5 to about 3.5, due to lactic acid formation.