Highly-brilliant time-resolved small-angle X-ray scattering (SAXS), operated at subsecond time resolution, has a potential to in situ reveal protein- and DNA-induced structural transitions in membrane assemblies upon binding and complexation of biomacromolecules to the lipid/water interfaces. Such high resolution experiments provide insights into temporary-living intermediate structures, occurring upon protein trafficking, and may evidence membrane deformations and curvature changes that are not accessible through steady-state microscopy imaging. We employed millisecond time-resolved SAXS, coupled to a rapid-mixing stopped-flow technique, for real time structural investigation of the kinetic pathway of assembly and complexation of plasmid DNA (pDNA) and fusogenic lipid carriers of nanochannelled organization (cubosome nanoparticles). pDNA upload into the highly hydrated channels of the cubosome carriers led to a fast nanoparticle-nanoparticle structural transition and lipoplex formation involving tightly packed pDNA. The rate constant of the pDNA/lipid membrane complexation was estimated from dynamic SAXS patterns recorded at 4 millisecond time resolution. The structural results evidenced that the phase transformation kinetics in the nanoparticulate system is influenced by the geometry of the lipid/water interfaces, their charge, and hydration. SAXS investigations of the protein anchoring on lipid membrane particles revealed, on the other hand, that the entrapped protein, depending on its concentration and amphiphilicity, may influence the interfacial curvature of the nanoassemblies and convert the internal nanostructure of channels into a different structural organization. The protein loading percentages, at which the formation of ordered Pn3m, La, and Ia3d phases was triggered inside the lipid nanoparticles, were quantitatively determined from time-resolved SAXS data.