We present a hybrid CMOS-based microfluidic system that combines magnetic actuation of microparticles with in situ optical detection using single photon avalanche diodes (SPADs). The decoupling of the principles used for actuation and sensing permits a high sensitivity with respect to detection and particle handling. Single magnetic microparticles are transported within a glass micro-capillary positioned over an array of actuation coils and are detected upon passage over a SPAD, where they block incident light and thus lower the photon count. Use of the photometry method allows the determination of the particle size, which, in combination with a simultaneous measurement of the particle velocity, enables us to estimate further particle properties, such as their magnetization.We present the successful manipulation, detection and evaluation of magnetic particles with diameters ranging from 1 to 30 um.