Starch is an inexpensive, easily accessible, and widespread natural polymer. Due to its properties and availability, this polysaccharide is an attractive precursor for sustainable products. Considering its exploitation in adhesives and coatings, the major drawback of starch is its high affinity towards water. This study aims to explain the influence of the silane-starch coating on the hydrophobic properties of paper. The analysis of the organosilicon modified starch properties showed an enhanced hydrophobic behavior, suggesting higher durability for the coatings. Molecules of silanes with short aliphatic carbon chains were easily embedded in the starch structure. Longer side chains of silanes were primarily localized on the surface of the starch structure. The best hydrophobic properties were obtained for the paper coated with the composition based on starch and methyltrimethoxysilane. This coating also improved the bursting resistance and compressive strength of the tested paper. A static contact angle higher than 115° was achieved. PDA analysis confirmed the examined material exhibited high barrier properties towards water. The results extend the knowledge of the interaction of silane compositions in the presence of starch.