A semiconductor device includes a metal-containing structure such as a copper-containing wire or plug and a composite capping layer formed over the metal-containing structure. The composite capping layer includes a manganese-containing layer disposed over the metal-containing structure, a silicon-containing low-k dielectric layer disposed over the manganese-containing layer, and an intermediate layer between the manganese-containing layer and the silicon-containing low-k dielectric layer. The intermediate layer is the reaction product of the manganese-containing layer and the silicon-containing low-k dielectric layer.