Nowadays, the microbial production of 1,3-propanediol (1,3-PD) is recognized as preferable to the chemical synthesis. However, finding a technological approach allowing the production of 1,3-PD in the membrane bioreactor (MBR) is a great challenge. In the present study, a ceramic ultrafiltration (UF) membrane (8 kDa) for treatment of 1,3-PD broths was used. It has been demonstrated that the membrane used provides the stable permeate flux that is necessary to ensure the stability of the fermentation process in MBR technology. It was noticed that the broth pH has a significant impact on both the final 1,3-PD concentration and permeate flux. Moreover, the feasibility of using NaOH for fouling control in the MBR was evaluated. It has been shown that 1% NaOH solution is effective in restoring the initial membrane performance. To the best of our knowledge, this study is the first to shed light onto the possibility of reducing the amount of the alkaline solutions generated during the MBR operation. Indeed, it has been found that 1% NaOH solution can be successfully used several times for both membrane cleaning and to stabilize the broth pH. Finally, based on the results obtained, the technological conceptions of the MBR technology were designed.