Prunus serotina Ehrh. is an alien invasive neophyte widespread in European forests. So far, no effective methods of its elimination have been developed. For this reason, the aim of our study was to determine how herbicides affect the morphological characteristics of pollen grains. This knowledge may be crucial to control this invasive species. The current study was carried out in a research area of 2.7 ha located in the Zielonka Forest near Poznań, Poland (N 52°31′58.016″, E 17°05′55.588″). We tested morphological differences among ten features of P. serotina pollen, based on the samples collected from 15 control trees compared to the 50 trees treated with five different herbicides. In total 1950 pollen grains were measured. We confirmed the adopted hypotheses of long-term herbicide influence on P. serotina pollen. Pollen grains from the control trees had a longer equatorial axis, were more elongated in shape and had the largest range of exine thickness compared to the pollen from the herbicide-treated samples. Exine thickness in the control sample was on average 0.74 µm, ranging from 0.42 to 1.19 µm. The average values and the ranges of this trait in the samples treated with herbicides were larger (e.g. average exine thickness was from 0.90 to 0.95 µm). There were differences in the P/E ranges of variability between the control and herbicide-treated samples. In the control sample the P/E ratio was 1.32–2.04 and elongated forms of pollen shapes prevailed, while in the herbicide-treated samples it ranged from 1.03 to 1.47. The share of deformed pollen grains in the herbicide-treated samples was lower than expected, ranging from 8.7 to 25.3%, while in the control samples it was 6%. Logo and Mustang turned out to be the most effective among the herbicides used in the described research. The two used application methods were found to have an effect on pollen quality.