Pectin aerogels, with very low density (around 0.1 g cm$^{-3}$ ) and high specific surface area (up to 600 m$^2$ g$^{-1}$), are excellent thermal insulation materials since their thermal conductivity is below that of air at ambient conditions (0.025 W m$^{-1}$ K$^{-1}$). However, due to their intrinsic hydrophilicity, pectin aerogels collapse when in contact with water vapor, losing superinsulating properties. In this work, first, pectin aerogels were made, and the influence of the different process parameters on the materials' structure and properties were studied. All neat pectin aerogels had a low density (0.04-0.11 g cm$^{-1}$), high specific surface area (308-567 m$^2$ g$^{-1}$), and very low thermal conductivity (0.015-0.023 W m$^{-1}$ K$^{-1}$). Then, pectin aerogels were hydrophobized via the chemical vapor deposition of methyltrimethoxysilane using different reaction durations (2 to 24 h). The influence of hydrophobization on material properties, especially on thermal conductivity, was recorded by conditioning in a climate chamber (25°C, 80% relative humidity). Hydrophobization resulted in the increase in thermal conductivity compared to that of neat pectin aerogels. MTMS deposition for 16 h was efficient for hydrophobizing pectin aerogels in moist environment (contact angle 115°) and stabilizing material properties with no fluctuation in thermal conductivity (0.030 W m$^{-1}$ K$^{-1}$) and density for the testing period of 8 months.