Among airborne biological contaminants, several pathogenic and/or allergenic fungi and bacteria can affect the health of horses and humans. Exposure to primary biological aerosol particles (PBAP) in the equine environment remains poorly understood, although environmental factors play a major role in the development of respiratory diseases and impaired performance in horses. This pilot study was conducted during a training course for young racers. Ambient and personal air samples provided original data on the microbial composition of PBAP in the riders’ immediate environment (stable, outdoor, riding arena), using culture-based and metagenomic approaches. The culture-based approach showed average levels of fungi and bacteria of 2.3 × 104 and 8.3 × 105 CFU/m3 respectively during training. Seventy-one and 50 fungal and bacterial species were respectively identified, while the metagenomic approach identified 211 and 285, respectively. It should be noted, however, that two-thirds of the bacterial and fungal genera were found by both approaches. Among these species, various pathogenic and/or allergenic fungi (Alternaria spp., Aspergillus spp., Cladosporium spp. and Lichtheimia ramosa) and bacteria (Aeromonas spp., Bacillus spp., Pseudomonas spp. and Staphylococcus spp.) were highlighted. This study underlines the value of the combined use of culture-based and metagenomic approaches to provide an overview of the distribution of different fungal and bacterial phyla, genera and species in the equine environment. Statistical analysis also suggests interactions between microbiological contaminants (bacteria and mold) and climatic parameters (rain, wind, temperature).