Forest canopies can buffer seedlings from extreme climate conditions. Yet, how disturbed forest canopies influence microclimate is not well understood, despite the important implications of microclimate for seedling establishment and post-disturbance successional trajectories. Better understanding of the relationship between a forest canopy and sub-canopy temperature and moisture conditions requires easily acquired and continuous forest canopy data, which is increasingly available due to new technology. Here, we measured canopy height using a remotely piloted aircraft (RPA) and monitored microclimate with low-cost temperature and soil moisture sensors in a sub-boreal forest impacted by fires of variable severity. We used regression models to investigate how differences in canopy height influenced microclimate variables. Mean growing season temperatures at -8 cm (soil), 0 cm (surface), and 15 cm (near-surface) relative to the ground surface were higher under shorter more disturbed canopies. Soil temperature was most sensitive to canopy height differences: linear models for the observed data range predicted a 2.0 °C increase in mean growing season soil temperature with every 10 m decrease in canopy height. We observed a weak negative relationship between canopy height and mean growing season soil moisture. We found that canopy height summarized at moderate resolution (15 m) better explained differences in temperature in our disturbed landscape. This work informs future methods to produce gridded microclimate datasets and outlines the impact of disturbed forest structure on microclimate variables. Our results show that the characteristics of the forest canopy remaining after a burn impact microclimates, which has important implications for post-fire ecosystems.