Nukadoko, a mixture of rice bran, salt, and water, is used for pickling vegetables to make Japanese traditional Nukazuke. Some Nukadoko manufacturers remove the bran-derived bacteria via heat treatment, but the effects of this treatment on the fermentation process are poorly understood. Herein, we investigate the effects of heat treatment and determine the contribution of bran-derived microorganisms to fermentation. We monitored pH and the counts of lactic acid bacteria (LAB), viable bacteria and yeasts in commercially unheated and heat-treated Nukadoko during the three 1-week fermentation periods. In heat-treated Nukadoko, the pH did not decrease during the first round of pickling. The LAB counts after the third fermentation round in heat-treated Nukadoko were substantially lower than those in unheated Nukadoko. External addition of LAB, Enterococcus faecalis, Leuconostoc mesenteroides, and Lactobacillus plantarum, to heat-treated Nukadoko did not accelerate the lactic acid fermentation of the first pickling. Native LAB in rice bran seemed to play an important role in the fermentation startup. During long-term refrigeration of Nukadoko without pickling, LAB and viable bacterial counts, and pH decreased; however, yeast counts increased. In heat-treated Nukadoko, such microbiological changes during storage were less than those observed in unheated Nukadoko.