Biofouling of artificial substrates is a well-known phenomenon that can negatively impact offshore industry operations as well as data collection in the ocean. Fouling communities worldwide have mostly been studied within the top 50 m of the ocean surface, while biofouling below this depth remains largely underreported. Existing methods used to study biofouling are labor intensive and expensive when applied to the deep sea. Here, we propose a simple and cost-effective modification of traditional methods for studying biofouling by mounting test plates on autonomous seafloor equipment and preserving them in ethanol upon retrieval for transport to the laboratory. This method can greatly advance our understanding of biofouling processes in the deeper ocean, including fouling community biodiversity, recruitment, and seasonality. We present two case studies from the Laptev Sea and the Sea of Okhotsk in support of this method. In the first study, we looked at fouling communities on the surfaces of ocean-bottom seismometers deployed for one year in the 36–350 m depth range. In the second study, we tested metal and plexiglass (poly(methyl methacrylate) plates mounted on autonomous bottom stations and found evidence of both micro- and macrofouling after three months of deployment. Our results demonstrate that various autonomous seafloor equipment can be used as supporting platforms for biofouling studies.