Because ancient proteins have a higher preservation potential than ancient DNA, proteomic studies can help shed light on the biology of some extinct biological groups that are beyond the reach of the field of ancient DNA. The oldest peptide discovered so far is part of the protein struthiocalcin (SCA-1) involved in eggshell mineralization and found within an ostrich egg from the Late Miocene Linxia Basin of Northwest China. It was originally hypothesized that SCA-1 was evenly distributed within the eggshell and was able to enter the fossil record for so long, because it was bound to calcite crystals. We conducted histological, scanning electron microscopy and Raman spectroscopic analyses on this same fossil egg to test if any protein or organic matter could be observed within specific regions of the eggshell and indeed bound to calcite crystals. Our results show that the eggshell is made entirely of calcite except at the base layer, which is made of mammillary knobs at least partially made of apatite. These knobs were secondarily phosphatized during diagenesis. After decalcification of this material, the fossilized mammillary knobs showed fibrous residues consistent in location and morphology with remnants of original organic material forming a network. This network was similar to the organic matrix observed in an extant ostrich eggshell with this same method. The results here suggest that SCA-1 may have been concentrated at the mammillary knobs, rather than evenly throughout the eggshell. Phosphatization may be another taphonomic process that favors organic preservation in deep-time. The paleoclimate and taphonomic environment of the Linxia Basin may have provided favorable conditions for the molecular preservation of this egg. More in-depth histochemical and mineralogical analyses will certainly increase our understanding of organic and ancient protein preservation in this basin.