Context Manure deposition during livestock export voyages contributes to air ammonia levels, potentially affecting human and animal health if not managed. Mitigation strategies may include increased air change rates and application of bedding. Aim This study examined the effect of bedding application rate (BAR) and air change rate (ACH) on air ammonia (NH3) concentrations and pad properties, including pad surface condition, pH, moisture, and pad ammonium (NH4+) concentrations, for intensively housed beef cattle. Methods Six 7-day runs were conducted with 72 Bos indicus cross steers (mean liveweight ± s.d. = 338 ± 32 kg) housed in respiration chambers by using a 3 × 3 factorial design. The BARs were set to 0%, 50%, and 100% of the Australian Standards for the Export of Livestock (ASEL), and ACH were varied at 20, 35, and 52. Air NH3 was measured twice daily at three heights. Pad surface condition was collected with the first air NH3 measurement. Video footage captured standing and lying behaviours for each steer. Pad samples were collected on the final day for pad chemical analysis. Key results The ACH of 20 changes per hour resulted in higher air NH3 concentration than ACH of 35 and 52. Higher BAR led to lower pad pH and moisture, with slightly lower pad NH4+ concentration in 100% and 50% BAR than 0% BAR. Although air NH3 concentration on Day 7 was positively correlated with pad NH4+ concentration, BAR had no marked effect on air NH3 concentration (within the temperature range of this experiment). Drier and firmer pad surfaces were associated with each high BAR and high ACH. Moreover, high BAR increased the frequency of lying behaviour in steers. Conclusions These findings indicated that NH3 can be mitigated by optimising air changes to minimise air NH3 concentration and utilising bedding to minimise pad NH4+. This offers practical solutions for intensively housed beef cattle, such as livestock export voyages to improve human and animal welfare onboard. Implications The study results emphasised the importance of optimising ACH to maintain low air NH3 concentrations in livestock export conditions. Although there was no evidence that BAR affects air NH3 directly, it reduced pad NH4+ and improved pad conditions for overall animal comfort and environmental quality in confined housing with sufficient air changes.