We investigate the effect of a microscopic three-body force on the proton and neutron superfluidity in the $^1S_0$ channel in $beta$-stable neutron star matter. It is found that the three-body force has only a small effect on the neutron $^1S_0$ pairing gap, but it suppresses strongly the proton $^1S_0$ superfluidity in $beta$-stable neutron star matter.