Short-rotation woody crops (SRWC) have the potential to make substantial contributions to the supply of biomass feedstock for the production of biofuels and bioproducts. This study evaluated changes in the fuel quality (moisture, ash, and heating value) of stored spring harvested shrub willow (Salix spp.) and hybrid poplar (Populus spp.) chips with respect to pile protection treatments, location within the storage piles, and length of storage. Leaf-on willow and poplar were harvested in the spring, and wood chips and foliage with moisture content in the range of 42.1% to 49.9% (w.b.) were stored in piles for five months, from May to October 2016. Three protection treatments were randomly assigned to the piles. The control treatment had no cover (NC), so piles were exposed to direct solar radiation and rainfall. The second treatment had a canopy (C) installed above the piles to limit direct rainfall. The final treatment had a canopy plus a dome aeration system (CD) installed over the piles. Covering piles reduced and maintained the low moisture content in wood chip piles. Within 30 days of establishment, the moisture content in the core of the C pile decreased to less than 30%, and was maintained between 24%–26% until the end of the storage period. Conversely, the moisture content in the NC piles decreased in the first two months, but then increased to the original moisture content in the core (>45 cm deep) and up to 70% of the original moisture content in the shell (<45 cm deep). For all the treatments in the tested conditions, the core material dried faster than the shell material. The higher heating value (HHV) across all the treatments increased slightly from 18.31 ± 0.06 MJ/kg at harvest to 18.76 ± 0.21 MJ/kg at the end of the storage period. The lower heating value (LHV) increased by about 50% in the C and CD piles by the end of the storage period. However, in the NC piles, the LHV decreased by 3% in the core and 52% in the shell. Leaf-on SRWC biomass stored in piles created in late spring under climatic conditions in central and northern New York showed differing moisture contents when stored for over 60–90 days. Overhead protection could be used to preserve or improve the fuel quality in terms of the moisture content and heating value if more than two months of storage are required. However, the implementation of such management practice will depend on whether the end users are willing to pay a higher price for dryer biomass and biomass with a higher LHV.