In biological cells, various transmembrane enzymes function as highly effective chemical reactors confined in space with characteristic length scales of tens of nanometers to micrometer. However, it is still challenging to quantitatively confine membranes in compact reactor platforms without losing their biochemical functions. Here, a simple and straightforward strategy towards the fabrication of a new flow-through reactor by the functional coating of porous silica microparticles with sarcoplasmic reticulum membranes is described. After a short incubation, the membranes achieve the homogeneous, full coverage of the particle surface, spanning across pores with the diameter of about 100 nm. By using the underlying pores as cavity reservoirs, transmembrane enzyme (Ca2+-ATPase) in the membrane retains their capability of ATP hydrolysis. This enables us to confine 1.1 m2 of native membranes containing a large amount of Ca2+-ATPase (approx. 10 nmol) in a column-packaged, flow-through reactor with merely 1.8 mL volume, which cannot be achieved by the reconstitution of proteins in artificial lipid membranes or condensation of membranes in suspensions. The distinct functional levels corresponding to different reaction buffers can be reproduced even after many buffer exchanges over 14 days, confirming the stability and reproducibility of the membrane-particle hybrid reactors.