Since ULSFOs are used in response to 0.1 % sulfur limits in maritime Emission Control Areas, there have been some returns of SCR catalysts showing a thin silicon dioxide layer on the catalyst surface. The catalyst activity decreased drastically after only 8000 h of engine operation. In this context, the presence of various silicon compounds in marine fuels and their effects on SCR catalysts were investigated. Experiments with silicon doped fuels and a fuel burner test bench revealed a fast catalyst deactivation due to organic silicon compounds (OSCs) in the fuels. Even low silicon fuel concentrations caused a significant loss of SCR activity. In this context, different OSCs had a similar impact on catalyst deactivation. Differences appeared under fuel variation. Organic silicon precursors in distillates induced stronger deactivation than in residual-containing fuels. The formation of silicon dioxide deposits from OSCs was shown by ATR-FTIR measurements. SEM-EDX analyses showed increasing silicon concentrations with layers of up to 5 µm on the catalyst surface with increasing operating hours and increasing OSC concentrations in the fuels. From the catalyst inlet to the outlet and when OSCs were mixed with soot and ash forming fuels, the silicon surface concentration decreased.