Switching the magnetic properties of organic semiconductors on a metal surface has thus far largely been limited to molecule-by-molecule tip-induced transformations in scanned probe experiments. Here we demonstrate with molecular resolution that collective control of activated Kondo screening can be achieved in thin-films of the organic semiconductor titanyl phthalocyanine on Cu(110) to obtain tunable concentrations of Kondo impurities. Using low-temperature scanning tunneling microscopy and spectroscopy, we show that a thermally activated molecular distortion dramatically shifts surface-molecule coupling and enables ensemble-level control of Kondo screening in the interfacial spin system. This is accompanied by the formation of a temperature-dependent Abrikosov-Suhl-Kondo resonance in the local density of states of the activated molecules. This enables coverage-dependent control over activation to the Kondo screening state. Our study thus advances the versatility of molecular switching for Kondo physics and opens new avenues for scalable bottom-up tailoring of the electronic structure and magnetic texture of organic semiconductor interfaces at the nanoscale.