For proteins, sacrifice a crystal that you wash free of unprecipitated material by dipping into precipitant solution and analyze by SDS-PAGE to see if both components are there. If one of the partners is not a protein, look for it by any other appropriate method that is sensitive enough
you could try to do an XRD analysis to investigate the crystal phases involved. For example, for co-crystals of inorganic minerals such as calcium sulfate co-precipitated with calcium carbonate, the XRD would show definitely the phases of both CaSO4 (3 phases) as well as those of CaCO3, e.g. calcite, aragonite, and vaterite. The XRD would show each of the phases qualitatively and quantitatively.