The fall armyworm (FAW), Spodoptera frugiperda, is a significant pest that causes economic losses worldwide. Many companies and research centers rear FAW to produce their microbiological-based products, such as viruses that target FAW. Nevertheless, colonies are vulnerable to collapsing, mainly due to uncontrolled and unexpected viral infections. In this work, dead FAWs exhibiting signs of viral infection were collected from unsuccessful attempts to propagate a baculovirus at a baculovirus production facility in Brazil. Total RNA was extracted and used to construct a cDNA library that was sequenced. The results showed the presence of five viruses, including three RNA viruses (alphanodavirus, rhabdovirus, and iflavirus) and two DNA viruses (densovirus and alphabaculovirus). To confirm the presence of the identified viruses in laboratory-reared FAWs, ten individual larvae from four accredited laboratories in Brazil were analyzed by RT-PCR with specific primers for each virus identified by sequencing, except the alphabaculovirus. Alphanodavirus and rhabdovirus were not detected in any of the four tested colonies, whereas the iflavirus was detected in two laboratories. A putative new densovirus was found in all samples. Accurate identification and timely detection of viruses that could disrupt the health of laboratory-reared insect colonies are crucial to ensure the production of high-quality biological products.