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Fischer–Tropsch (FT) synthesis was carried out in a 3D printed stainless steel (SS) microchannel microreactor using bimetallic Co-Ru catalysts on three different mesoporous silica supports. CoRu-MCM-41, CoRu-SBA-15, and CoRu-KIT-6 were synthesized using a one-pot hydrothermal method and characterized by Brunner–Emmett–Teller (BET), temperature programmed reduction (TPR), SEM-EDX, TEM, and X-ray photoelectron spectroscopy (XPS) techniques. The mesoporous catalysts show the long-range ordered structure as supported by BET and low-angle XRD studies. The TPR profiles of metal oxides with H2 varied significantly depending on the support. These catalysts were coated inside the microchannels using polyvinyl alcohol and kinetic performance was evaluated at three different temperatures, in the low-temperature FT regime (210–270 °C), at different Weight Hourly Space Velocity (WHSV) in the range of 3.15–25.2 kgcat.h/kmol using a syngas ratio of H2/CO = 2. The mesoporous supports have a significant effect on the FT kinetics and stability of the catalyst. The kinetic models (FT-3, FT-6), based on the Langmuir–Hinshelwood mechanism, were found to be statistically and physically relevant for FT synthesis using CoRu-MCM-41 and CoRu-KIT-6. The kinetic model equation (FT-2), derived using Eley–Rideal mechanism, is found to be relevant for CoRu-SBA-15 in the SS microchannel microreactor. CoRu-KIT-6 was found to be 2.5 times more active than Co-Ru-MCM-41 and slightly more active than CoRu-SBA-15, based on activation energy calculations. CoRu-KIT-6 was ~3 and ~1.5 times more stable than CoRu-SBA-15 and CoRu-MCM-41, respectively, based on CO conversion in the deactivation studies. Keywords: Fischer-Tropsch synthesis; mesoporous silica based catalysts; kinetic studies; 3-D printed microchannel microreactor