Superconductors and magnetic materials, including molecules, are key ingredients for quantum and advanced spintronic applications. However, only a little is known about how these materials are mutually influenced at their interface in hybrid architectures. Here, we show that a single layer of magnetic molecules, the Terbium(III) bis-phthalocyaninato (TbPc2) complexes, deposited on a superconducting Pb(111) surface is sensitive to the topology of the intermediate state of the superconductor, namely to the presence and evolution of superconducting and normal domains due to the magnetic field screening and penetration. The evidence of this sensitivity is found in the magnetisation dynamics of the TbPc2 sub-monolayer in its paramagnetic regime showing the fingerprint of the topological hysteresis of the superconducting substrate. This study reveals the great potentialities hold by thin layers of magnetic molecules for sensing local magnetic field variation in hybrid molecular/superconductor architectures, including spin resonators or spin injection devices for spintronics applications.