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The mega-diverse, Mediterranean-type fynbos biome may be vulnerable to future changes in climate and associated fire regimes, in particular to increasing summer-drought intensity and associated potential expansion of adjacent semi-arid vegetation types. Studying Holocene vegetation dynamics at the fynbos-succulent karoo boundary may provide insights into the resilience or sensitivity of fynbos to climate change. In this study, fossil pollen, non-pollen palynomorphs and charcoal data spanning 5500 to -50 cal. yr BP were generated from an accelerator mass spectrometer (AMS) radiocarbon-dated sediment core extracted directly at the present-day fynbos-succulent karoo biome boundary at Groenkloof, a site in the Kamiesberg Mountains of Namaqualand, South Africa. Contrary to expectations, during the Mid-Holocene Altithermal from 5480 to 4025 cal. yr BP, fynbos and fire thrived through summer moisture subsidies associated with enhanced sub-tropical easterly flow. Subsequent cooling from 4025 to 2005 cal. yr BP resulted in enhanced summer drought and overall fynbos biome contraction, though woody fynbos shrubs persisted through physiological adaptations to drought. Desert succulents typical of the succulent karoo, such as those of Aizoaceae and Crassulaceae, failed to colonise the emergent niche space, resulting in dominance of an ambiguous grassy, asteraceous fynbos. More recent wetting associated with the Little Ice Age’ Holocene temperature minima from 695 to 100 cal. yr BP prompted a resurgence in fynbos abundance, but frequent fire driven by pastoralists appears to have reduced the fynbos community’s functional diversity. Palaeoecological data from the Kamiesberg suggest that both climatic buffering of mountain refugia and high physiological resistance among certain fynbos taxa have contributed to the biome’s long-term resilience. Summer rainfall associated with the sub-tropical easterlies has been key in maintaining eastern fynbos refugia in past interglacial temperature maxima. The data also suggest that pre-historic land use and resulting fire-regime manipulations have resulted in the development of a taxonomically and functionally simplified alternative fynbos ecosystem state.