Longitudinal shifts in pollen onset, duration, and intensity are public health concerns for the growing number of individuals with pollen sensitization. National analyses of long-term pollen changes are influenced by how a plant's main pollen season (MPS) is defined. Prior Swiss studies have inconsistently applied MPS definitions, leading to heterogeneous conclusions regarding the magnitude, directionality, and significance of multi-decade pollen trends. We examined national pollen data in Switzerland between 1990 and 2020, applying six MPS definitions (2 percentage-based and 4 threshold-based) to twelve relevant allergenic plants. We analyzed changes in pollen season using both linear regression and locally estimated scatterplot smoothing (LOESS). For 4 of the 12 plant species, there is unanimity between definitions regarding earlier onset of pollen season (p < 0.05), with magnitude of 31-year change dependent on specific MPS definition (hazel: 9-18 days; oak: 5-13 days; grasses: 8-25 days; and nettle/hemp: 6-25 days). There is also consensus (p < 0.05) for modified MPS duration among hazel (21-104% longer), nettle/hemp (8-52% longer), and ash (18-38% shorter). Between-definition agreement is highest for MPS intensity analysis, with consensus for significant increases in seasonal pollen quantity (p < 0.05) among hazel, birch, oak, beech, and nettle/hemp. The largest relative intensification is noted for hazel (110-146%) and beech (162-237%). LOESS analysis indicates that these multi-decade pollen changes are typically nonlinear. The robustness of MPS definitions is highly dependent on annual pollen accumulation, with definition choice particularly influential for long-term analysis of low-pollen plants such as ragweed. We identify systematic differences between MPS definitions and suggest future aerobiologic studies apply multiple definitions to minimize bias. In summary, national pollen onset, duration, and intensity have shifted for some plants in Switzerland, with MPS definition choice affecting magnitude and significance of these variations. Future public health research can determine whether these temporal and quantitative pollen changes correlate with longitudinal differences in population pollen sensitization.