<p>Airborne pollen and fungal spores (bioaerosols) are important for organisms’ reproduction and at the same time they are also bio-indicators of environmental change and they may have serious impacts on human health, as they can trigger respiratory symptoms. Monitoring bioaerosols in urban settings provides information on the quality of the atmospheric environment, which can be used by urban planners for adopting measures towards optimizing the ecosystem services of the urban greenery. As people reside, work and recreate both outdoors and indoors and at different heights above the ground, three-dimensional bioaerosol monitoring is necessary to capture this spatial variability. The aim of this research was to assess bioaerosol diversity and abundance in a typical urban setting, namely along the height gradient of a multi-storey building of workplaces, in Thessaloniki, Greece, both outdoors and indoors. Two portable Hirst-type volumetric samplers were used simultaneously at the two settings and at four sampling heights, from near ground level and up to 25&#xa0;m, twice per week, during January-December 2020, collecting a total of 392 outdoor and 392 indoor samples. Both the diversity and abundance of pollen grains and fungal spores decreased with increasing height; this was more pronounced for herbaceous plants (e.g., Poaceae and Urticaceae, <i>p</i> &lt; 0.001) and all fungi (<i>p</i> &lt; 0.001), which implies sources of their particles mostly of local origin, whereas woody plants showed variable patterns suggesting medium or long-range transport. Pollen and fungal spore total abundance was lower indoors than outdoors for all sampling heights, while indoor-outdoor dissimilarity (<i>β</i>-diversity) increased with height for both bioaerosol types. Our findings highlight the complexity of bioaerosol diversity and abundance at different heights and the need for height-specific three-dimensional monitoring.</p>