The presence of nestlings influences the microclimate inside avian nesting cavities. We explored the relationship between temperature and relative humidity and the abundance of ectoparasites and gas concentrations in blue tit nest boxes during the nestling period by comparing two years with differing climatic conditions. In the second year, we also manipulated the temperature and humidity inside the nest boxes. The average temperature in nest boxes was colder during 2016 than 2017; in the latter, even warmer conditions were attained due to the experimental manipulation of temperature. Carbon dioxide (CO2) concentration in the forest air was slightly lower in 2016 than 2017. However, in both years, the CO2 concentration of nest box air was higher than that of forest air, with 2017 showing a greater difference. Differences in brood size, larger in 2016, did not explain the difference in CO2 concentration. However, CO2 concentration was higher in nestboxes in the warmer year implying that at higher temperatures, organic matter decomposition likely accelerates, releasing more CO2 into the atmosphere. By contrast, CH4 concentration in nest-box air, which was similar in both years, was lower than that in forest air, particularly in the wettest and coldest year. Different relationships were found between the abundance of different ectoparasites and the temperature, relative humidity, and gas concentration measured at different days of nestling age. For example, a positive association is observed between flea larval abundance and temperature at nestling day 8, but a negative one is observed for mites under the same microclimate conditions. Moreover, a negative relationship was observed between the abundance of mites, midges, and blackflies and CH4 concentration at different nestling ages. These results suggest that changes in climatic conditions can also affect the concentrations of CH4 and CO2 inside and outside nest boxes, which in turn differentially affect ectoparasite abundance.