The final microstructure of a phase separating and gelling biopolymer mixture is affected by physical confinement, because the structure evolution is limited by the surrounding surfaces. Here, we used various confining geometries such as microdroplets, parallel cover glasses, and networks of cellulose fibers to analyze the structure evolution and final morphology of mixtures of whey protein isolate (WPI) and gellan gum. The results were evaluated by confocal laser scanning microscopy (CLSM) and 2D fast Fourier transform (FFT) image analysis. This showed that the final morphology within the restricted geometry is determined by the characteristic wavelength of the bicontinuous bulk microstructure in relation to the dimensions of the confinements. The growth of the characteristic wavelength in the WPI-gellan gum system has two different regimes, which are similar in the bulk phase and large microdroplets. The growth is then kinetically trapped by the gelation. In microdroplets with a smaller dimension than the characteristic bulk wavelength, the growth of the spinodal structure is observed to collapse as the characteristic wavelength approaches the microdroplet diameter. This results in a core-shell structure with WPI present at the interface. Furthermore, 3D reconstructions of CLSM images from the parallel glass confinement showed that the bicontinuous structure is converted to columnar structures interconnecting two wetting layers at the glass surfaces. Similar columnar structures are observed between cellulose fibers. The present findings demonstrate that it is important to understand the impact of confinement on phase separation and gelation in order to control the final microstructure.