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Harvesting adherent cells from microcarriers has become one of the major challenges of the downstream bioprocessing at large scale the current method has high maintenance and operation cost, which are the results of frequent clogging, due to cell lysing effect and microcarrier cake formation on membrane-based technology. These problems hugely impede the adaptation of microcarriers technologies in large-scale cell culture and hampered the supply of cells to the clinical need. Here, we describe two 3D printing-based methods to fabricate inertial microfluidic devices for separating adherent cells from microcarriers which overcome the above-mentioned limitations. The spiral devices are employed to separate mesenchymal stem cells from the microcarriers with 99% microcarrier removal rate and 77% cell recovery rate in one round of separation., (© 2021. Springer Science+Business Media, LLC.)