Ostrich eggshell is a favoured substrate for amino acid geochronology, yielding consistent results and thought to approximate a closed system with respect to protein diagenesis. We found that the intra-crystalline fraction in ostrich eggshell is more challenging to isolate than that from mollusc shells, requiring 72 h oxidative treatment with NaOCl, resulting in a loss of up to half of the whole-shell protein. Through high temperature studies we have shown that under continuous leaching conditions approximately 99% of the intra-crystalline amino acids are resistant to leaching. Furthermore, high temperature experiments of the intra-crystalline proteins at pH 5, 7 and 9 have shown that this fraction is unaffected by pH changes over this range. This study confirms that the intra-crystalline protein fraction in OES may approximate a closed system. The intra-crystalline amino acids have been shown to follow predictable patterns of hydrolysis and racemization for all amino acids studied. Most amino acids showed some conformity to pseudo reversible first order reaction kinetics for racemization over limited D/L ranges, but hydrolysis was generally described poorly by first order kinetics. We therefore tried a new scaling method to determine relative reaction rates, estimated by applying scaling factors to overlap the observed rates of racemization (or hydrolysis) at the different temperatures, with the advantage of not forcing a linear relationship with respect to time. Using apparent first order kinetics, constrained power functions and scaling methods, we estimated the Arrhenius parameters (activation energy, E_A and frequency factors, A) for both hydrolysis and racemization. The different methods for the estimation of reaction rates can give significantly different, but equally plausible, activation energies. This study reinforces previous work that indicates we need to understand the underlying mechanisms in order to estimate accurate kinetic parameters.