In this study pulsed electric field (PEF) was used to increase accumulation of iron and vitamin B12 in Saccharomyces cerevisiae cells, which were then used to produce flakes. The yeast was enriched in two ways: only by adding iron salt (FeCl3·6H2O) and vitamin B12 to the culture medium and by additional application of PEF. Three trials of yeast flakes were prepared: C1 (control, not supplemented), C2—with B12 and iron salt and not treated with PEF, and P—with B12 and iron salt and treated with PEF (for 20 min at 10 μs pulse width, voltage of 1500 V, a number of pulses 1200 and field frequency 1 Hz). The use of PEF resulted in higher iron and vitamin B12 accumulation, respectively, 2.5- and 1.4-fold for the sample P compared to the sample C2. The potential bioavailability of iron from yeast flakes was 10.13% and vitamin B12–4.31%, and the quality of this product was rated good by a sensory panel.