Novel fire mitigation treatments that chip harvested biomass on site are increasingly prescribed to reduce the density of small-diameter trees, yet the ecological effects of these treatments are unknown. Our objective was to investigate the impacts of mechanical thinning and whole tree chipping on Pinus ponderosa (ponderosa pine) regeneration and understory plant communities to guide applications of these new fuel disposal methods. We sampled in three treatments: (1) unthinned forests (control), (2) thinned forests with harvested biomass removed (thin-only), and (3) thinned forests with harvested biomass chipped and broadcast on site (thin + chip). Plots were located in a ponderosa pine forest of Colorado and vegetation was sampled three to five growing seasons following treatment. Forest litter depth, augmented with chipped biomass, had a negative relationship with cover of understory plant species. In situ chipping often produces a mosaic of chipped patches tens of meters in size, creating a range of woodchip depths including areas lacking woodchip cover within thinned and chipped forest stands. Thin-only and thin + chip treatments had similar overall abundance and species richness of understory plants at the stand scale, but at smaller spatial scales, areas within thin + chip treatments that were free of woodchip cover had an increased abundance of understory vegetation compared to all other areas sampled. Relative cover of non-native plant species was significantly higher in the thin-only treatments compared to control and thin + chip areas. Thin + chip treated forests also had a significantly different understory plant community composition compared to control or thin-only treatments, including an increased richness of rhizomatous plant species. We suggest that thinning followed by either chipping or removing the harvested biomass could alter understory plant species composition in ponderosa pine forests of Colorado. When considering post-treatment responses, managers should be particularly aware of both the depth and the distribution of chipped biomass that is left in forested landscapes.