Quaternary palaeopalynological records collected throughout the Iberian Peninsula and species distribution models (SDMs) were integrated to gain a better understanding of the historical biogeography of the Iberian Abies species (i.e. Abies pinsapo and Abies alba). We hypothesize that SDMs and Abies palaeorecords are closely correlated, assuming a certain stasis in climatic and topographic ecological niche dimensions. In addition, the modelling results were used to assign the fossil records to A. alba or A. pinsapo, to identify environmental variables affecting their distribution, and to evaluate the ecological segregation between the two taxa. For the estimation of past Abies distributions, a hindcasting process was used. Abies pinsapo and A. alba were modelled individually, first calibrating the model for their current distributions in relation to the present climate, and then projecting it into the past—the last glacial maximum (LGM) and the Middle Holocene periods—in relation to palaeoclimate simulations. The resulting models were compared with Iberian‐wide fossil pollen records to detect areas of overlap. The overlap observed between past Abies refugia—inferred from fossil pollen records—and the SDMs helped to construct the Quaternary distribution of the Iberian Abies species. SDMs yielded two well‐differentiated potential distributions: A. pinsapo throughout the Baetic mountain Range and A. alba along the Pyrenees and Cantabrian Range. These results propose that the two taxa remained isolated throughout the Quaternary, indicating a significant geographical and ecological segregation. In addition, no significant differences were detected comparing the three projections (present‐day, Mid‐Holocene and LGM), suggesting a relative climate stasis in the refuge areas during the Quaternary. Our results confirm that SDM projections can provide a useful complement to palaeoecological studies, offering a less subjective and spatially explicit hypothesis concerning past geographic patterns of Iberian Abies species. The integration of ecological‐niche characteristics from known occurrences of Abies species in conjunction with palaeoecological studies could constitute a suitable tool to define appropriate areas in which to focus proactive conservation strategies.