The stable operation of the anaerobic digestion of waste activated sludge (WAS) is threatened by numerous emerging contaminants. Meanwhile, the extensive microplastic pollution increased the environmental exposure risk of plasticizer benzyl butyl phthalate (BBP), the BBP content has reached a substantial level in WAS. However, the effect of BBP on WAS anaerobic digestion is still unknown. Here we show that high-level BBP brings on anaerobic digestion upset. The presence of 10.0 mg/L BBP (in sludge with 17,640 ± 510 mg/L TSS) led to deferred cell lysis, which was confirmed by the results of continuous parallel factor analysis of dissolved organic matter and the liberation of lactate dehydrogenase. Further, the deferred cell rupture was confirmed associate with prophage activation during WAS anaerobic digestion. Besides solubilization, the hydrolysis, acetogenesis and methanogenesis were also affected by the addition of BBP. The long-term effects of BBP revealed that the dominant microbial structure in anaerobic digester was stable, but the abundance of many functional microorganisms was changed, including short chain fatty acid producers and consumers. This work highlights one of the susceptibility mechanisms for WAS anaerobic digestion processes and provides new perspectives for the comprehensive assessment of emerging contaminant's environmental risks. Display omitted •BBP at 10 mg/L brings on the disorder of SCFA accumulation.•BBP affects the solubilization, hydrolysis, acetogenesis and methanogenesis.•BBP causes cell lysis after 4 days and increases the number of virus-like particles.•The anaerobic digestion upset is attributed to prophage activation.