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Microplastics (MP) have been proposed as a vector for pathogenic microorganisms in the freshwater environment. The objectives of this study were (1) to compare the fecal indicator growth in biofilms on MP and material control microparticles incubated in different wastewater fractions and (2) to compare MP biofilm, natural microparticle biofilm, and planktonic cell susceptibility to disinfection by peracetic acid (PAA). Biofilms were grown on high‐density polyethylene, low‐density polyethylene, polypropylene MP or wood chips (as a material control) and incubated in either wastewater influent or pre‐disinfection secondary effluent. Reactors were disinfected with PAA, biofilms were dislodged, and fecal coliform and E. coli were cultivated. Fecal indicators were quantifiable in both MP and wood biofilms incubated in the wastewater influent but only on the wood biofilms incubated in secondary wastewater effluent. More fecal coliform grew in the wood biofilms than MP biofilms, and the biofilms grown on MP and woodchips were more resistant to disinfection than planktonic bacteria. Thus, it may be possible to refer to the disinfection literature for fecal indicators in biofilm on other particles to predict behavior on MP. Treatments that remove particles in general would help reduce the potential for fecal indicator bypass of disinfection.