The mite and fungal biota associated with the mountain pine beetle (MPB) (Dendroctonus ponderosae Hopk.) may not be stable throughout an irruptive event. In congeneric beetles, variations in the frequency of their associated organisms affect population trends and similar effects may occur in MPB. We studied fungi and mite trends in a declining irruptive MPB population as it attacked three different pine hosts in the Colorado Front Range. During the study, we found two new associates including one biologically relevant mite and one beneficial blue-stain fungus. Fungi hyperphoretic on mites were also documented. This included beneficial and potentially detrimental species to the MPB. The frequency of several organisms varied between some years or pine hosts but not within male or female beetles. A large increase of Trichouropoda sp. and T. ips mites trended inversely with the declining beetle population, while a decrease in the beneficial blue-stain fungi trended similarly to the declining beetle population. We discuss the interactions and potential effects of phoretic biota in relation to (1) the MPB associates’ population trends, (2) the MPB incursions into cooler areas, and (3) the redundancy of blue-stain fungi carried by the MPB holobiont. These findings increase our knowledge of the mechanisms that influence MPB populations.