We discuss the production of $D$-mesons and $J/psi$ in high multiplicity proton-proton and proton-nucleus collisions within the Color-Glass-Condensate (CGC) framework. We demonstrate that the modification of the LHC data on $D$ and $J/psi$ yields in high multiplicity events relative to minimum bias events arise from a significant enhancement of the gluon saturation scales of the corresponding rare parton configurations in the colliding protons and nuclei. For a given event multiplicity, we predict these relative yields to be energy independent from $sqrt{s}=200$ GeV at RHIC to the highest LHC energies.