We combine experiments and numerical simulations to investigate the emergence of clogging in a system of interacting paramagnetic colloidal particles driven against a disordered landscape of larger obstacles. We consider a single aperture in a landscape of immobile silica particles which are irreversibly attached to the substrate. We use an external rotating magnetic field to generate a traveling wave potential which drives the magnetic particles against these obstacles at a constant and frequency tunable speed. Experimentally we find that the particles display an intermittent dynamics with power law distributions at high frequencies. We reproduce these results by using numerical simulations and show that clogging in our system arises at large frequency, when the particles desynchronize with the moving landscape. Further, we use the model to explore the hidden role of flexibility in the obstacle displacements and the effect of hydrodynamic interactions between the particles. We also consider numerically the situation of a straight wall and investigate the range of parameters where clogging emerges in such case. Our work provides a soft matter test-bed system to investigate the effect of clogging in driven microscale matter.