Surface engineering with polydopamine coatings has been considered a promising surface functionalisation tool. However, it is difficult to control the self-polymerisation for polydopamine formation, which usually causes severe interparticle aggregation. In this study, polydopamine self-polymerisation was controlled by adjusting its reducing environment using a reductant (NaBH4) to fabricate mixed cellulose ester (MCE)/polydopamine membranes. An oxidising environment using NaIO4 was additionally tested as the control. The results showed that a thin polydopamine coating with small polydopamine particles was formed on the skeleton frameworks of the MCE membrane with NaBH4, and the self-polymerisation rate was suppressed. The polydopamine coating formed in the reducing environment facilitated excellent water transport performance with a water permeance of approximately 400 L · m−2 · h−1 · bar−1 as well as efficient organic foulant removal with a bovine serum albumin rejection of approximately 90%. In addition, the polydopamine coating with NaBH4 exhibited both excellent chemical stability and anti-microbial activity, demonstrating the contribution of the reducing environment to the performance of the MCE/polydopamine membranes. It shows significant potential for use in water purification.