The rock shelter site Klipfonteinrand 1 (KFR1), located on the edge of southern Africa’s Fynbos biome, was initially excavated by John Parkington in 1969. Due to difficulties resolving the stratigraphic sequence, the lack of age estimates, and generally poor organic preservation, the Middle Stone Age (MSA) components of the site have received limited attention. In this paper we report on the re-excavation, dating, palaeoecology, and cultural sequence recovered from a trench placed adjacent to Parkington’s original excavation. The refined sequence includes three stratigraphically distinct MSA components: a Howiesons Poort component dating to ~69 ka, and two earlier MSA components dating to ~85 ka and ~156 ka. These are overlain by two younger components dated to the late Pleistocene and early Holocene. Bedrock morphology at the site is complex, and the oldest component appears to be restricted to a small area of relatively deep (1.9 m) sediment accumulation towards the centre of the sheltered area. Phytoliths suggest limited change in floral communities near the site across the lowest three units—which include parts of marine isotope stages (MIS) 6, 5, and 4—reflecting the characteristic stability of the Fynbos biome. The stone artefacts in the oldest MSA component include large blades that are absent from the overlying strata, and that may be a distinct element of late MIS 6 technology in the area. Interestingly, neither the early MSA nor early Holocene components we describe here were encountered in the rear trench at the site, 3 m away, which instead produced a sequence dominated by marine isotope stage 2 occupation. KFR1 presents new insights into the archaeology of the earlier MSA in southern Africa, while also providing a cautionary note on the discontinuous and spatially variable nature of rock shelter occupation in the region.