Vibration-mediated Kondo effect was the focus of many theoretical papers in recent years. However, suitable experimental systems that serve as a controllable test-bed for both Kondo physics and electron-vibration interactions are rare. Molecular junctions formed in a break-junction setup are natural candidates for this task due to the ability to modify the coupling to the electrodes and vibration energies of the molecule in the junction. Here, we focus on a vibration-mediated Kondo system in molecular junctions composed of silver electrodes and copper-phthalocyanine molecules. Using differential conductance spectroscopy the system is characterized in details as a function of temperature, magnetic field and inter-electrode separation. Our experimental results shed light on the interplay between the Kondo system and the inelastic conductance induced by vibrations.