Ichnofossils from two compound paleosols in the middle Miocene Pawnee Creek Formation (PCF) of northeastern Colorado, U.S.A., indicate a diverse soil ecosystem that included plants, invertebrates, and vertebrates. The 2–4 m thick paleosols are characterized by blocky textures, shallow depth calcareous horizons overlying silty bioturbated horizons, calcareous nodules, dense mats of fine (< 1 mm diameter) rhizoliths in the upper 750 mm, 5–10 mm diameter rhizoliths up to 3 m deep, and burrows 2–800 mm in diameter. PCF paleosols likely formed within a shrubland and grassland environment. Ichnofossils include backfilled burrows with chambers and cocoons; simple backfilled burrows; small-diameter boxworks; cylindrical burrow complexes; large, scratch-marked burrow networks; large downward spiraling burrows; large subhorizontal burrows; and gravel-filled tunnels and chambers. These unique PCF ichnofossils include three new ichnogenera and eight new ichnospecies. Ichnofossils attributed to ground beetles, ants, reptiles, and mammals represent a complex variety of behaviors including temporary to permanent dwelling, nesting, and food storing. Rhizoliths and burrows used to interpret media consistency, organic content, soil moisture, and water-table level are tiered from shallow, intermediate, to deep levels within paleosols with respect to physical and biological factors. Separate bioturbated intervals permits the recognition of two different paleosols that otherwise might not have been recognized. Such well-developed paleosols with high densities of terrestrial burrows have substantial sequence stratigraphic significance since they define surfaces of low sedimentation, base level, and accommodation. The PCF ichnofossil assemblages represent at least three distinct ichnocoenoses. The Kladosystemites ichnocoenosis, with Kladosystemites, Polychoredrites, Parowanichnus, and 1–10 mm diameter rhizoliths, is present in the upper profile of well-drained, consolidated, and nutrient-rich paleosols with dense concentrations of small-to-large plants at the surface. The Beaconites ichnocoenosis, with Beaconites, Katarrhedrites, and 5–10 mm rhizoliths, is present in the lower profile of moderately organic paleosols above the influence of the water table but subject to seasonally variable saturated and unsaturated conditions due to precipitation. The Daimonelix ichnocoenosis, with Daimonelix, Beaconites, small-to-large Katarrhedrites, and 5–10 mm diameter rhizoliths, is present in the lower profile of very organic-rich paleosols generally above the influence of the water table but subject to seasonally variable saturated and unsaturated conditions. Integration of data from body fossils, ichnofossils, paleosols, and sedimentary environments provides new insight into Neogene ecosystems. Paleosol properties combined with the ichnofossil distribution, abundance, and diversity indicates that Miocene PCF paleosols formed under a seasonal climate subject to wide variation in temperature and precipitation. The diverse assemblage of burrow morphologies records adaptation of the local fauna to these environmental conditions. The response of soil ecosystems to short- and long-term changes in climate is, therefore, vital to any study of the effects of climate change in the geologic record.