Mushrooms are highly perishable products, typically possessing a shelf-life of up to 8 days at 4 °C. To maintain mushroom quality during storage low O2- (1–5%) and elevated CO2-levels (<12%) are recommended. However, this is not an easy task as mushrooms respire, thereby consuming O2 and releasing CO2. Headspace gas composition was measured daily non-invasively using optically based O2 and CO2 sensors inserted in each pack and correlated to microbiological and physicochemical characteristics. Equilibrium levels of O2 = 11.58% and CO2 = 10.7% were achieved after 18.5 and 41.5 h, respectively. The microbiological results showed Pseudomonas spp. as the main spoilage microorganism. The polyphenol oxidase (PPO) activity decreased (P < 0.05) throughout storage. Mushroom degradation was caused by microbiological and enzymatic activity, and these parameters correlated well with changes in colour, pH, weight loss and sensory analysis. This study confirmed that optically based sensor systems can be used to rapidly monitor non-destructively headspace gases of packed mushrooms continuously.