Deciphering pollen assemblages from alpine speleothems holds potential to provide unique information about past vegetation in rapidly changing environments. Here, we reconstruct subsurface aerosol transport at Milchbach cave (Switzerland, 1840 m asl) based on the pollen content of two Holocene stalagmites. We demonstrate that pollen is chiefly associated with bacterially mediated calcite fabrics, typical of a well-ventilated cave system. In contrast, pollen is absent from columnar calcite fabrics confirming that hydrological transport is not a significant process for the incorporation of pollen into speleothems at Milchbach cave. Our results support significant changes in the subsurface ventilation regime, which can be associated with the waxing and waning of Upper Grindelwald glacier. Pollen assemblages obtained from six carbonate sub-samples attest the presence of a mixed deciduous forest in the Grindelwald valley during the early and middle Holocene, in agreement with coeval regional pollen records. This study demonstrates that even small amounts of calcite (0.3–2.8 cm3) are capable of delivering pollen spectra representative of the original vegetation if sufficiently elevated deposition fluxes are provided.