We provide a comprehensive theoretical description of low-energy quantum transport for a Coulomb-Majorana junction, where several helical Luttinger liquid nanowires are coupled to a joint mesoscopic superconductor with finite charging energy. Including the Majorana bound states formed near the ends of superconducting wire parts, we derive and analyze the Keldysh phase action describing non-equilibrium charge transport properties of the junction. The low-energy physics corresponds to a two-channel Kondo model with symmetry group SO(M), where M is the number of leads connected to the superconductor. Transport observables, such as the conductance tensor or current noise correlations, display non-trivial temperature or voltage dependences reflecting non-Fermi liquid behavior.