This study aimed to determine the effects of carbon dioxide concentration in modified atmosphere packaging (MAP) on the quality criteria and shelf life of whole wheat flour bread. Four different concentrations of CO2 and N2 gases (30% CO2 + 70% N2, 50% CO2 + 50% N2, 70% CO2:30% N2 and 100% CO2) were applied to the bread samples, which were packaged with PA/EVOH/LDPE (polyamide/ethylene vinyl alcohol/low‐density polyethylene). The samples were stored at room temperature (25°C ± 1°C) for 13 days. The control group was packaged using BOPP (bi‐oriented polypropylene) under atmospheric air as in traditional current use. The effects of MAP on headspace gas analysis, pH, moisture content, water activity, water‐holding capacity, blue value, hardness, total mould and yeast count and sensory evaluation were analysed on days 0, 3, 4, 5, 7, 10 and 13. The results showed that the most effective gas combination in extending the shelf life of whole wheat bread was 100% CO2, and its shelf life was 10 days, whereas it was only 3 days for the control group. Increasing concentrations of CO2 significantly affected mould and yeast growth. As the CO2 concentration increased, the bread exhibited higher water‐holding capacity and blue values, which are important indicators for bread staling. An improved preservation of sensory properties was observed in proportion to increasing CO2 concentrations. However, the CO2 gas concentration did not affect the hardness of the bread. Overall, the study suggests that MAP technology, particularly using 100% CO2, can effectively extend the shelf life of whole wheat flour bread without the need for preservatives, not only extending the microbiological shelf life but also increasing the sensory shelf life. The species that grew in air‐packaged samples were suppressed under modified atmosphere conditions and chalk mould fungi were the dominant and shelf life‐impacting species in the MAP samples. These findings could be beneficial in reducing bread wastage, which is a critical issue in today's society due to the limited shelf life of bread caused by rapid microbiological deterioration or staling.