The increase in the frequency of peatland fires is due to both global climate change and deliberate human activity. The primary aim of the study was to investigate the structure of microbial communities and nematodes before and after a peat bog fire, as well as to analyse the relationships between food web components. Hydrological and physicochemical parameters were analysed during the period before the fire (2018 and 2019) and after the fire (2020 and 2021—2, 4, 8, and 12 months after the fire). The fire clearly modified the physicochemical properties of the peat bog, increasing the temperature, pH, conductivity, and concentrations of biogenic compounds and organic matter. It also caused a pronounced deterioration in oxygen conditions. The fire clearly modified the qualitative and quantitative structure and functioning of microbial food webs. This was reflected in a decrease in the species number and abundance of testate amoebae, with various groups of microbes showing pronounced fluctuations during the study period. The functioning of food webs in peatlands after fires is still very little understood, although an understanding of the functioning of these habitats, which increasingly undergo this type of catastrophe due to global climate change, is crucial.