Competition for adsorption sites between atmospheric moisture and volatile organic compounds (VOCs) can significantly impact the VOC removal performance of novel metal–organic framework adsorbent such as MIL-101. MIL-101 has high surface area and high porosity, but its inherent hydrophilicity hinders selectivity for hydrophobic organic species in the presence of atmospheric moisture. In this study, a vapor phase deposition of polydimethylsiloxane (PDMS) was used to create more hydrophobic MIL-101 composites. The external hydrophobicity of the composites was evaluated through water contact angle measurements whereas the internal hydrophobicity was assessed using a vapor-sorption based hydrophobicity index. After an optimized vapor deposition time of 0.25 hr employing a low molecular weight PDMS, a MIL-101 composite with enhanced internal hydrophobicity and intact porosity was fabricated. The composite’s efficacy for VOC capture was investigated through toluene-water vapor co-adsorption experiments which involved vapor adsorption at 40% RH and at two toluene concentrations: 0.5% P/P0 and 10% P/P0. At 0.5% toluene P/P0, the new composite exhibited almost 60% higher adsorption capacity and 34% higher overall capture rate relative to pristine MIL-101 due to the presence of a hydrophobic PDMS layer which delayed the onset of water condensation in the mesopores. At 10% toluene P/P0, the new composite’s overall toluene uptake was 2.8 times higher than activated carbon, but slightly lower than pristine MIL-101. This new composite also showed excellent structural stability and adsorption performance after 10 sorption/desorption cycles. The superior performance of the MIL-101-PDMS composite could be utilized to selectively remove toluene from real world humidities and VOC concentrations.