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The suitability of reed- and straw-bale houses for the temperate climate zone was assessed. The influence of indoor climate indicators (relative humidity, internal humidity load of the borders, CO2, temperature, mould index) and the microbial community was evaluated on air quality in the bedrooms. No similar studies on indoor air quality have been reported previously. In order to fulfil the set aim: (1) indoor air quality parameters (relative humidity, CO2, and temperature) in air and at two different heights in the walls were measured; (2) air quality was tested in the bedrooms of the studied houses, and the microbial species in air and walls were determined; (3) it was determined how the microbial communities of indoor air in the straw and reed-bale buildings influence indoor air quality in bedrooms. Internal moisture was higher in the reed-bale buildings (from 0.46 g m–3 to 3.42 g m–3 in summer and from 0.62 g m–3 to 2.73 g m–3 in winter). Microbial species in the air and walls of the studied houses were determined. Moulds belonging to four different genera were identified during this study (Alternaria, Aspergillus, Penicillium, and Cladosporium) in the bedrooms. Higher colony-forming unit (CFU) values were registered. The indoor air of the straw-bale and reed-bale build-ings included more colonies than the outside air, but this did not affect indoor air quality.