The weak interaction between neutrons and matter allows neutrons to penetrate materials easily and as a result, it is feasible to use complex sample environments for in situ studies. On the other hand, to investigate a large casein gel particle during digestion, the gel should be under the neutron beam within a 1 mm cell maximum in order to avoid a phenomenon called ‘multiple scattering’. This study examined options for in situ analysis of a gel structure during digestion: (A) attaching the gel structure to the surface of the sample cell or holding it within a mesh while passing digestive enzymes through, (B) trapping the gel in a Teflon grid, or (C) blending the gel particles. It was determined that blending gels and utilising a flow setup is the optimal method for ensuring that the internal structure of gel particles does not change significantly between the 1 nm and 20 μm length scale.