The design and fabrication of materials that exhibit both semiconducting and magnetic properties for spintronics and quantum computing has proven difficult. Important starting points are high-purity thin films as well as fundamental theoretical understanding of the magnetism. Here we show that small molecules have great potential in this area, due to ease of insertion of localised spins in organic frameworks and both chemical and structural purity. In particular, we demonstrate that archetypal molecular semiconductors, namely the metal phthalocyanines (Pc), can be readily fabricated as thin film quantum antiferromagnets, important precursors to a solid state quantum computer. Their magnetic state can be switched via fabrication steps which modify the film structure, offering practical routes into information processing. Theoretical calculations show that a new mechanism, which is the molecular analogue of the interactions between magnetic ions in metals, is responsible for the magnetic states. Our combination of theory and experiments opens the field of organic thin film magnetic engineering.