A yolk–shell nanocomposite composed of a magnetic mesoporous anatase TiO₂ (Fe₃O₄@mTiO₂) core, a medium cavity and an outermost mesoporous silica (mSiO₂) shell was successfully fabricated. Due to a combination of the strong magnetic response, improved diffusion of peptides, numerous affinity sites towards phosphopeptides and the size-exclusion effect, the nanocomposite demonstrated high enrichment efficacy and selectivity towards endogenous phosphopeptides from human serum.