Marine propulsion systems, like sterndrive systems, must be protected from corrosion degradation. In particular, in the case of aluminium alloy parts, a protective cycle consisting in a surface pretreatment and an organic coating system are often applied. Traditionally, chromate based pretreatments are often applied on aluminium alloys in aggressive environments for the protective ability of chromate layers, together with the self-healing and adhesion promotion ability. The toxicity of chromium hexavalent is pressed to find new environmentally friendly solutions. In this paper, new results concerning different protective cycles for marine propulsion systems are presented. New surface pretreatments, including zircofluotitanates, chromium(III) treatments and silane layers, were characterised in conjunction with two different organic layers: waterborne paints and powder coatings. All the systems are free from organic solvents and toxic active pigments. By electrochemical measurements and salt spray exposure, it was possible to optimise the protective cycle with low environmental impact for the protection of aluminium components for marine propulsion systems, proving final performance comparable with the traditional systems containing chemicals with high environmental impact.