Addressing notorious and worldwide Microcystis blooms, mechanical algae harvesting is an effective emergency technology for bloom mitigation and removal of nutrient loads in waterbodies. However, the absence of effective methods for removal of cyanobacterial toxins, e.g., microcystins (MCs), poses a challenge to recycle the harvested Microcystis biomass. In this study, we therefore introduced a novel approach, the "captured biomass-MlrA enzymatic MC degradation", by enriching microcystinase A (MlrA) via fermentation and spraying it onto salvaged Microcystis slurry to degrade all MCs. After storing the harvested Microcystis slurry, a rapid release of extracellular MCs occurred within the initial 8 h, reaching a peak concentration of 5.33 μg/mL at 48 h during the composting process. Upon spraying the recombinant MlrA crude extract (about 3.36 U) onto the Microcystis slurry in a ratio of 0.1% (v/v), over 95% of total MCs were degraded within a 24-h period. Importantly, we evaluated the reliability and safety of using MlrA extracts to degrade MCs. Results showed that organic matter/nutrient contents, e.g. soluble proteins, polysaccharides, phycocyanin and carotenoids, were not significantly altered. Furthermore, the addition of MlrA extracts did not significantly change the bacterial community composition and diversity in the Microcystis slurry, indicating that the MlrA extracts did not increase the risk of pathogenic bacteria. Our study provides an effective and promising method for the pre-treatment of harvested Microcystis biomass, highlighting an ecologically sustainable framework for addressing Microcystis blooms.