Daily monitoring of airborne fungal spores was carried out for the first time in Al Khor city, Qatar, using a Hirst type 7-day recording volumetric spore trap, from May 2017 to May 2019. During the sampling period, the annual and monthly fluctuations, as well as intradiurnal variations of airborne fungal spore concentrations, were evaluated. Cladosporium, followed by Alternaria, were the spore types most abundant in the atmosphere of the city, with a strong interannual variability in the atmospheric concentrations being observed. The Annual Spore Integrals (ASIns) were 3334 and 1172 spore * day/m3 (2017–2018), and 6796 and 1538 spore * day/m3 (2018–2019) for Cladosporium and Alternaria, respectively. Total daily spore concentrations showed significantly positive correlations with mean, minimum, and maximum temperatures but significantly negative correlations with relative humidity. However, due to the scarce rainfalls’ days, we did not find a statistically significant correlations between Cladosporium and Alternaria spore concentrations and this parameter. Despite this, the spore peaks were strongly related to precipitations that occurred during the previous month. In general, no significant correlations were found with wind speed but, regarding wind direction, the higher percentage of spores were collected when wind blows from the 4th quadrant (NW). According to the intradiurnal pattern, Cladosporium fungal spores displayed their maximum daily concentration during 8:00–10:00 h in the morning, with a second peak in the afternoon, while for Alternaria, the maximum peaks were observed between 08:00 and 14:00 h. Because no consistent previous aerobiological studies exist from Qatar, the aim of this study is to define the seasonality and intradiurnal behaviour of these two airborne fungal spore and the role that, in such arid scene, the meteorological parameters play on the spore concentrations.