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Aerial and respiratory tract-associated bacterial diversity has been scarcely studied in broiler production systems. This study examined the relationship between the environmental air and birds’ respiratory microbiome, considering a longitudinal sampling. Total viable bacteria and coliforms in the air were quantified, and the 16S rRNA gene was sequenced from tracheal and air samples obtained through a novelty protocol. Air results showed a decrease in coliforms over time. However, at week 3, we reported an increase in coliforms (from 143 to 474 CFUc/m³) associated with litter management. Additionally, 16S rRNA gene results indicated a distinctive air microbial community, associated primarily with <i>Bacillota</i> phylum particularly of the <i>Bacilli</i> class (>58%), under all conditions. Tracheal results indicated a predominance of <i>Escherichia coli/Shigella</i> at the beginning of the productive cycle, shifting toward the middle and end of the cycle to <i>Gallibacterium</i>. However, at week 3, the dominance of <i>Escherichia coli/Shigella</i> (>99.5%) associated with litter aeration by tumbling stood out. Tracheal and air samples displayed a statistically different community structure, but shared differentially abundant features through time: <i>Enterococcus</i>, <i>Gallibacterium</i>, and <i>Romboutsia ilealis</i>. These results indicate the impact of production management protocols on the birds’ respiratory system that should be considered a breakpoint in poultry farm health.