The wet season atmosphere in the central Amazon resembles natural conditions with minimal anthropogenic influence, making it one of the rare pre-industrial-like continental areas worldwide. Previous long-term studies have analyzed the properties and sources of the natural Amazonian background aerosol. However, the vertical profile of the planetary boundary layer (PBL) has not been assessed systematically. Since 2017, such a profile assessment has been possible with the 325 m high tower at the Amazon Tall Tower Observatory (ATTO), located in a largely untouched primary forest in central Amazonia. This study investigates the variability of submicrometer aerosol concentration, size distribution, and optical properties at 60 and 325 m height in the Amazon PBL. The results show significant differences in aerosol volumes and scattering coefficients in the vertical gradient. The aerosol population was well-mixed throughout the boundary layer during the daytime but became separated upon stratification during nighttime. We also found a significant difference in the spectral dependence of the scattering coefficients between the two heights. The analysis of rainfall and related downdrafts revealed changes in the aerosol populations before and after rain events, with absorption and scattering coefficients decreasing as optically active particles are removed by wet deposition. The recovery of absorption and scattering coefficients is faster at 325 m than at 60 m. Convective events were concomitant with rapid increases in the concentration of sub-50 nm particles, likely associated with downdrafts. We found that the aerosol population near the canopy had a significantly higher mass scattering efficiency than at 325 m. It was also observed a clear spectral dependence, with values for λ = 450, 525 and 635 nm of 7.74±0.12, 5.49±0.11and 4.15±0.11 m² g^−1, respectively, at 60 m, while at 325 m, the values were 5.26±0.06, 3.76±0.05 and 2.46±0.04 m² g^−1, respectively. The equivalent aerosol refractive index results, which were obtained for the first time for the wet season in central Amazon, show a slightly higher scattering (real) component at 60 m compared to 325 m, of 1.33 and 1.27, respectively. In contrast, the refractive index’s absorptive (imaginary) component was identical for both heights, at 0.006. This study shows that the aerosol physical properties at 60 and 325 m height are different, likely due to aging processes, and strongly depend on the photochemistry, PBL dynamics, and aerosol sources. These findings provide valuable insights into the impact of aerosols on climate and radiative balance and can be used to improve the representation of aerosols in global climate models.