Climate change is disrupting phenology and interaction patterns of natural ecosystems, but also human activities that modify land-uses have a direct impact, especially on species distribution and loss of biodiversity. The objective of this study is to evaluate the impact of climate and land-use changes on phenology and airborne pollen spectrum in a Mediterranean natural area, dominated by Quercus Forest and ‘dehesa’, in the South of the Iberian Peninsula. 61 different pollen types were identified over a 23-year period (1998–2020), mainly from trees and shrubs, such as Quercus, Olea, Pinus or Pistacia, and from herbaceous plants, such as Poaceae, Plantago, Urticaceae or Rumex. A comparison of pollen data from the first years of the study (1998–2002) up recent years (2016–2020), showed a substantial decrease in the relative abundance of pollen from autochthonous species associated with natural areas, such as Quercus or Plantago. However, the relative abundance of the pollen from cultivated ones such as Olea and Pinus, which is used for reforestation has increased. Regarding flowering phenology trends, our analyses revealed variations between −1.5 and 1.5 days per year. Taxa showing an advance phenology were Olea, Poaceae and Urticaceae, whereas Quercus, Pinus, Plantago, Pistacia or Cyperaceae experienced delayed pollination.Meteorological trends in the area generally resulted in an increase in both minimum and maximum temperatures, along with a decrease in precipitations. Changes in pollen concentration and phenology were correlated with changes in air temperatures and precipitation, although the positive or negative influence varied for each pollen type. The results suggest that climate change together with those motivated by land cover changes lead by human activities are having an impact on the phenology and pollen concentration, with the related consequences on pollination and therefore biodiversity more concerning in threatened areas as the Mediterranean Basin.