Essentially all animal life interacts closely with an array of microorganisms such as bacteria and viruses, which can have both beneficial and harmful effects. The advancement of high-throughput molecular biology approaches (DNA and RNA sequencing) has led to an ongoing boom in investigating the composition and functions of microbial communities (microbiota) associated with a wide range of animal taxa, including insects. As this area of investigation has blossomed, such research on indoor urban insect pests has lagged more widely studied species. However, over the last several years, significant strides have been made in understanding the diversity and biological roles of microbes associated with such insects. This review highlights and discusses recent key findings, focusing on bed bugs and cockroaches, two of the most prolific globally invasive indoor insect pests. Advances in this area of research have long-term implications for public health and for the development of novel pest control approaches.