Microfluidics is a very attractive discipline for implementing more versatile high‐throughput screening methods to improve enzymes. However, state‐of‐the‐art microfluidics set‐ups are mainly devoted to screening enzymes in solution, while screening of enzyme immobilization protocols using microfluidics is scarce. In this work, a microreactor device is designed, fabricated and applied to test different heterogeneous biocatalysts with transaminase activity. This microsystem set‐up can be operated in two different modes: packed‐bed (PBR) and fluidized (FBR) microreactors without exchanging the sample. Using the same sample to run the two modes, the fidelity of the comparison is increased between the two fluid dynamic regimes. Moreover, by testing different carriers under different modes, a Histagged transaminase is found from Pseudomonas fluorescens immobilized on agarose porous microbeads functionalized with cobalt‐chelates and operated as FBR maximizes the STY, and minimizes the equilibration times. This device exemplifies the potential of microreactors for prototyping more efficient heterogeneous biocatalysts.