The Amazon Basin, which plays a critical role in the carbon and water cycle, is under stress due to changes in climate, agricultural practices, and deforestation. The effects of thermodynamic and microphysical forcing on the strength of thunderstorms in the Basin (75–45°W, 0–15°S) were examined during the pre-monsoon season (mid-August through mid-December), a period with large variations in aerosols, intense convective storms, and plentiful flashes. The analysis used measurements of radar reflectivity, ice water content (IWC), and aerosol type from instruments aboard the CloudSat and CALIPSO satellites, flash rates from the ground-based Sferics Timing and Ranging Network, and total aerosol optical depth (AOD) from a surface network and a meteorological re-analysis. After controlling for convective available potential energy (CAPE), it was found that thunderstorms that developed under dirty (high-AOD) conditions were 1.5 km deeper, had 50% more IWC, and more than two times as many flashes as storms that developed under clean conditions. The sensitivity of flashes to AOD was largest for low values of CAPE where increases of more than a factor of three were observed. The additional ice water indicated that these deeper systems had higher vertical velocities and more condensation nuclei capable of sustaining higher concentrations of water and large hydrometeors in the upper troposphere. Flash rates were also found to be larger during periods when smoke rather than dust was common in the lower troposphere, likely because smoky periods were less stable due to higher values of CAPE and AOD and lower values of mid-tropospheric relative humidity. Plain Language Summary The Amazon Basin, which plays an important role in the carbon and water cycle, is under stress due to changes in climate, agricultural practices, and deforestation. The Basin includes a rainforest in the northwest and a mix of deforested areas, savannah-type vegetation, and agriculture in the southeast. The effects of instability and aerosol loading on thunderstorms in the Basin (75–45°W, 0–15°S) were examined during mid-August through mid-December, a period with large variations in aerosols, intense convective storms, and plentiful flashes. The analysis used measurements of radar reflectivity, ice water content (IWC), and aerosol type from instruments aboard the CloudSat and CALIPSO satellites, flash rates from the ground-based Sferics Timing and Ranging Network, and AOD from a surface network and a meteorological re-analysis. After controlling for convective available potential energy, a measure of instability, it was found that thunderstorms that developed under dirty (high-AOD) conditions were approximately 1.5 km deeper, had 50% more IWC, and more than two times as many flashes as storms that developed under clean (low-AOD) conditions. Flash rates were also found to be larger during periods when smoke rather than dust was common in the lower troposphere, likely because these periods were less stable.