Fly infestations threaten farming and livestock operations, contributing to animal irritation and the spread of serious diseases. In this study, the application of Bacillus velezensis PHP1601 (Bacillales: Bacillaceae) treatments (105 and 1010 endospore g−1) to pig manure slurries was evaluated as a means of controlling fly reproductive cycles. Two cycles of fly emergence were evaluated over a 33 days period for each replicated trial. For both treatments, the first emergence event resulted in a significant reduction in the percentage of flies emerging compared to an un-treated control. Extended monitoring of the biocontrol containers revealed that fly emergence was completely eliminated by the time that a second round of fly emergence was observed for the control. A B. velezensis-specific real-time PCR method was developed and used to assess the population dynamics of the applied biocontrol agent over the course of the experiment. Strain PHP1601 remained viable in the manure and cell numbers increased by several orders of magnitude. REP-PCR fingerprinting was used to confirm the clonality of endospores recovered from the manure. Fly species recovered from the trials were identified by cytochrome oxidase gene barcode sequencing. Several species of veterinary and medically significant flies were identified. They were all deemed to be susceptible to treatments with PHP1601 and constituted part of the strain's host range. The study demonstrated the effectiveness of B. velezensis PHP1601 as a promising biocontrol agent for controlling fly infestations under conditions similar to its intended use.