Disclosed are systems for treating a substrate comprising a deoxidizing composition and a coating composition. The deoxidizing composition comprises a Group IVA metal and/or a Group IVB metal and free fluoride, optionally may comprise a homopolymer or copolymer comprising a phosphorous-containing monomeric subunit, and has a pH of 1.0 to 3.0. The coating composition comprises first and second components and elastomeric particles. The first component comprises an epoxy-containing compound (E1) and/or an epoxide-functional adduct (E2). The second component comprises a diamine and/or a polyamine comprising a cyclic ring (A2) and/or an amine-functional adduct (A3). The present invention is also directed to methods of making the compositions, methods of coating a substrate, and coated substrates.