The extent of racemization (total hydrolysable amino acids) of aspartic acid, glutamic acid and valine provide a geochronological framework to assign relative and numeric ages, and examine the taphonomy of the sedimentary infill of Apollo 11 Rockshelter, Namibia. Based on the analysis of 37 ostrich (Struthio camelus) eggshell samples from the rockshelter sedimentary succession, three aminogroups are identified and may be correlated with oxygen isotope records from marine and ice cores. Aminogroup A spans the interval from 80,000 ± 12,000 years ago [late Marine Isotope Stage (MIS) 5a] through to the late Holocene (2000 ± 300 years). A significant diastem is identified below − 65 cm separating the lower portion of the rockshelter sediments (that were deposited predominantly by natural depositional processes), from the overlying succession. Although a human presence is generally evident throughout the whole succession, the post-diastem succession records an increasing influence of humans on sediment accumulation. Two aminogroups were identified in the sediments beneath the diastem based on contrasting extents of racemization. Pooled mean ages (representing minimum ages) for aminogroups B and C are 180,000 ± 10,000 years and 236,000 ± 18,000 years respectively, and are significantly different at the 2-sigma level. The amino acid derived numeric ages indicate an early Middle Stone Age (MSA) for the lower portion of the sedimentary succession within the rockshelter. Collectively, these ages attest to a long, but punctuated record of sediment accumulation within Apollo 11 Rockshelter. At several levels within the anthropogenically-dominated succession (layers A to T), fragments of ostrich eggshell show a disproportionately high extent of racemization in relation to their depth of burial and signify the combined effects of heating and their reworking. The reworked eggshell fragments represent a small component of the assemblage, and the overall results for aminogroup A indicate that the sedimentary succession shows a high degree of stratigraphical integrity. Reworking of sedimentary constituents is not evident in aminogroups B and C. The age for the basal layers Y and Z from Apollo 11 is one of the oldest dates for an Early MSA inventory without Acheulean elements in Southern Africa, a period that is otherwise poorly known.