We consider the Kondo effect in Y-junctions of anisotropic XY models in an applied magnetic field along the critical lines characterized by a gapless excitation spectrum. We find that, while the boundary interaction Hamiltonian describing the junction can be recasted in the form of a four-channel, spin-1/2 antiferromagnetic Kondo Hamiltonian, the number of channels effectively participating in the Kondo effect depends on the chain parameters, as well as on the boundary couplings at the junction. The system evolves from an effective four-channel topological Kondo effect for a junction of XX-chains with symmetric boundary couplings into a two-channel one at a junction of three quantum critical Ising chains. The effective number of Kondo channels depends on the properties of the boundary and of the bulk. The XX-line is a “critical” line, where a four-channel topological Kondo effect can be recovered by fine-tuning the boundary parameter, while along the line in parameter space connecting the XX-line and the critical Ising point the junction is effectively equivalent to a two-channel topological Kondo Hamiltonian. Using a renormalization group approach, we determine the flow of the boundary couplings, which allows us to define and estimate the critical couplings and Kondo temperatures of the different Kondo (pair) channels. Finally, we study the local transverse magnetization in the center of the Y-junction, eventually arguing that it provides an effective tool to monitor the onset of the two-channel Kondo effect.