A magnetic microparticle-based bioassay requires the separation of the microparticles from the sample matrix, after the microparticles have specifically captured the target of interest. For the implementation of such an assay in water-in-oil droplet segmented flow microfluidics, the particles must be separated from the aqueous sample droplets during a purification step. Current magnetic separation methods pose limits to purification, as only a limited part of the sample volume is removed in the purification step. Combining asymmetric droplet splitting in a T-junction-shaped microfluidic channel with magnetic separation, as induced by a permanent magnet positioned close to the microfluidic channel, is a promising and elegant solution for extracting the magnetic microparticles. However, retaining a high separation efficiency is a challenge and yet untried. In this paper, we describe a microfluidic and magnetic setup to separate superparamagnetic microparticles from the sample droplets, removing up to 90 % of the original sample volume in a single purification step, while keeping the separation efficiency constant. First, the conditions for particle aggregation, attraction and immobilization are determined and used to predict good separation conditions. Second, the magnetic forces at the splitting zone on the microfluidic chip are simulated for different permanent magnet positions and orientations; hereafter, the most promising setups are experimentally realized in polydimethylsiloxane microchannels, tested and the results considering different splitting regimes compared.