This metadata file presents two palaeoecological records of spores of coprophilous fungi (SCF) processed from lake sediment cores collected from Laguna La Yeguada, Panama. The data were collected to investigate the effects of two methods for processing and quantifying SCF in the lab to provide a direct comparison of the available methodological approaches for SCF preparation and quantification in palaeoecological studies. The data were collected for the PhD research titled: Ecological consequences of Pleistocene megafaunal declines in the Neotropics (https://gtr.ukri.org/projects?ref=studentship-2859430), funded by https://gtr.ukri.org/projects?ref=NE/S007504/1