The aim of this study was to assess the microbiological quality of air in three horse riding centers differing in the horse keeping systems. The air samples were collected in one facility with free-range horse keeping system and two with box stalls of different sizes. The samples were collected over a period of 3 years (2015–2017), four times per year (spring, summer, autumn, winter) to assess the effect of seasonal changes. The prevalence of aerobic mesophilic bacteria, mold fungi, actinomycetes, Staphylococcus spp., and Escherichia coli was determined by the air collision method on Petri dishes with appropriate microbiological media. At the same time, air temperature, relative humidity, and particulate matter concentration (PM10, PM2.5) were measured. It was found that the horse keeping system affects the occurrence of the examined airborne microorganisms. Over the 3-year period of study, higher temperature and humidity, as well as particulate matter concentration—which notoriously exceeded limit values—were observed in the facilities with the box-stall system. The air sampled from the largest horse riding center, with the largest number of horses and the box-stall system of horse keeping, was also characterized by the heaviest microbiological contamination. Among others, bacteria from the following genera: Staphylococcus spp., Streptococcus spp., Bacillus spp., and E. coli and fungi from the genera Aspergillus, Fusarium, Mucor, Rhizopus, Penicillium, Trichothecium, Cladosporium, and Alternaria were identified in the analyzed samples.