E. coli is a commonly used host for generating large quantities of human recombinant proteins. These proteins are often considered free of post-translational modifications (PTMs); however, a subset of the produced proteins can incorporate modifications derived from the host bacterial enzymes. Here, we used tandem mass spectrometry to identify inadvertent PTMs on human recombinant proteins produced in E. coli. As proof of concept, we identified bacteria-mediated PTMs on human tau and EFhd2 proteins, which we used in in vitro studies to understand their role in Alzheimer's disease (AD). Some of the identified PTMs have been previously associated with AD while others are novel. Additionally, we identified E. coli proteins that co-purified with these human recombinant proteins even after several purification steps.