Typically, after large stand-replacing fires in mid-elevation Sierra Nevada forests, dense shrub fields occupy sites formerly occupied by mature conifers, until eventually conifers overtop and shade out shrubs. Attempting to reduce fuel loads and expedite forest regeneration in these areas, the USDA Forest Service often disrupts this cycle by the logging of fire-killed trees, replanting of conifers and killing of shrubs. We measured the effects of these treatments on live and dead fuel loads and alien species and modeled potential fire behavior and fire effects on regenerating forests. Sampling occurred in untreated, logged and herbicide-treated stands throughout the Sierra Nevada in four large fire areas 4–21 years after stand-replacing fires. Logging fire-killed trees significantly increased total available dead fuel loads in the short term but did not affect shrub cover, grass and forb cover, alien species cover or alien species richness. Despite the greater available dead fuel loads, fire behavior was not modeled to be different between logged and untreated stands, due to abundant shrub fuels in both logged and untreated stands. In contrast, the herbicide treatment directed at shrubs resulted in extremely low shrub cover, significantly greater alien species richness and significantly greater alien grass and forb cover. Grass and forb cover was strongly correlated with solar radiation on the ground, which may be the primary reason that grass and forb cover was higher in herbicide treated stands with low shrub and tree cover. Repeat burning exacerbated the alien grass problem in some stands. Although modeled surface fire flame lengths and rates of spread were found to be greater in stands dominated by shrubs, compared to low shrub cover conifer plantations, surface fire would still be intense enough to kill most trees, given their small size and low crown heights in the first two decades after planting.