We present a CMOS-based hybrid microfluidic system that combines the manipulation of magnetic microparticles through a magnetic field with in situ optical detection via single photon avalanche diodes (SPADs). Magnetic particles are actuated within a glass micro-capillary and are detected upon passage over the SPAD, where they block incident light and thus lower the photon count. The optical sensors, which are not influenced by the magnetic actuation forces, allow detecting the presence of magnetic particles of 30, 5 and 1 µm diameter, while being able to distinguish between different sizes.