Polydopamine (PDA) as a mussel-inspired poly(catechol)amine with the capability of being coated on a variety of surfaces has attracted the attention of many researchers. In this article, the integrity of PDA nano-layer in living soil was studied in depth. To this end, polydopamine was coated on the surface of the synthesized magnetic Fe3O4 nanoparticles (Fe3O4@PDA) and incubated in the magnetic particles-free soil for different periods of up to 120 days. According to the obtained results, the PDA biodegradation commences within the first week, and then due to the surface precipitation of Ca and Si compounds on the PDA, the biodegradation slows down. Also, the results revealed that PDA despite its 47% degradation in the soil environment within 120 days, has little effect on the soil’s biological properties. The mass loss of the coating due to the biodegradation in the living soil was modeled by different models including the Kulkarni model, the first-order model, and the second-order model, which the results showed that the first-order model could describe the data much better, indicating that the hydrolysis reactions of the polymer chain have occurred by both enzymatic catalyzes and hydroxyl ions in soil and the bond scission rate decreased exponentially with time. The released moieties from the PDA to the soil were determined by gas chromatography-mass spectrometry (GC–MS) to mainly be trimethyl cyclopentanol, methyltetrahydrofuryl glucine, methylpentyl pentanoate, and methyltriazol amine.Graphical Abstract