Feast-famine moving bed biofilm reactors (MBBRs) have shown high potential for removing organic micropollutants from wastewater. However, the relationship between biofilm community during feast-famine adaptation and micropollutant removal is yet unclear. In this study, we determined the biotransformation kinetics of 36 micropollutants and characterized the microbial communities in an MBBR during a 71-day adaptation period of feast-famine regime (raw/effluent wastewater). The feast-famine regime significantly changed the biodegradation rate constants (k) of 24 micropollutants in different ways: 66 times enhanced degradation for propranolol, while more than 10 times for atenolol, metoprolol, tramadol and venlafaxine, less than 2.8 times for losartan, iomeprol and iohexol were detected. 25–60 days of adaptation time was needed to reach the maximum k. Biofilm accumulated during the adaptation, but the kDNA (k relative to the biofilm with DNA concentration as a proxy for kbiomass) of most micropollutants (except propranolol, metoprolol and venlafaxine) declined. This might indicate that the proliferation of potential degraders for micropollutants was slower than other microorganisms under the feast-famine regime. The microbial community changed significantly during the first 8 days of operation, followed by a relatively steady evolution towards the enrichment of nitrifiers until day 71. A multivariate statistical correlation analysis revealed that the development of occurrence of 88 individual taxonomic groups were found to exhibit a significant positive correlation to the kDNA of micropollutants (p < 0.05, r > 0.5), which represent potential biomarkers linking to biotransformation of micropollutants. These results fill the knowledge gaps between dynamics of biofilm communities and micropollutant removal in the feast-famine regime, which is essential for designing highly efficient MBBR.