Isolated microspore culture in vitro (IMC) is an advanced technique for producing doubled haploids. We developed a modified microspore isolation method for the Brassicaceae family, which exceeds the results obtained by a standard microspore isolation method. We found that the new method allows an increase in the percentage of microspores at the embryogenic stage of development in the culture. In the spring rapeseed ‘Ratnik’ culture the percentage of microspores increases from 66.7% to 73%, and in the European radish ‘RBK’ from 34% to 61.9%. Moreover, the new method of microspore isolation made it possible to expand the range of linear bud sizes (from 3.5–4.0 to 3.0–4.5 mm for spring rapeseed ‘Ratnik’) suitable for IMC technology. In addition, the new method of microspore isolation reduced the debris in the preparation of spring rapeseed ‘Ratnik’ and European radish ‘RBK’ by 2.4 and 15 times, respectively. The best results were shown on Sareptian mustard No. 72, where the yield of embryoids increased by 7.5 times. Remarkably, the new method of microspore isolation allowed us to obtain the first embryoids of red cabbage No. 428, whereas no embryoids were obtained using the standard method of microspore isolation. In summary, the new method of microspore isolation allows an increase in the efficiency of IMC technology for Brassicaceae family crops.