With the recent dawn of the multi-messenger astronomy era a new window has opened to explore the constituents of matter and their interactions under extreme conditions. One of the pending challenges of modern physics is to probe the microscopic equation of state (EoS) of cold and dense matter via macroscopic neutron star observations such as their masses and radii. Still unanswered issues concern the detailed composition of matter in the core of neutron stars at high pressure and the possible presence of e.g. hyperons or quarks. By means of a non-perturbative functional renormalization group approach the influence of quantum and density fluctuations on the quark matter EoS in $beta$-equilibrium is investigated within two- and three-flavor quark-meson model truncations and compared to results obtained with common mean-field approximations where important fluctuations are usually ignored. We find that they strongly impact the quark matter EoS.