Stability of integrated fixed-film indigenous microalgal-bacterial consortium (IF-IMBC) requires further investigation. This study focused on the influence of short-term stagnation (STS), caused by influent variations or equipment maintenance, on IF-IMBC. Results showed that the IF-IMBC system experienced initial inhibition followed by subsequent recovery during STS treatment. Enhanced organics utilization was believed to contribute to system recovery. It is proposed that the attached IMBC possessed greater stress resistance. On the one hand, a higher increase in bacteria potentially participating in organic degradation was observed. Moreover, the dominant eukaryotic species significantly decreased in suspended IMBC while its abundance remained stable in the attached state. On the other hand, increased abundance for most functional enzymes was primarily observed in the attached bacteria. This fundamental research aims to bridge the knowledge gap regarding the response of IMBC to variations in operational conditions.