Soil microorganisms maintain vital soil processes in agroecosystems, simultaneously affected by agricultural intensification and climate change in a negative way. Organic amendments such as biochar and compost have the potential to counteract these adverse effects on soil microorganisms. However, often only a snapshot is studied while seasonal changes also play an important role. To reveal the temporal dynamics of the soil microorganisms after organic application, we have studied two fields treated with either a single dose of biochar (Field A: 0 vs. 10,900 kg C ha‑1) or a yearly compost application (Field B: 0 vs. 2,000 kg C ha‑1 year‑1). Soil samples were taken every five weeks for over a year. Using metabarcoding, we showed that biochar did not affect the bacterial community of the soil. This can be explained by the fact that the soil provided a stable environment for the bacterial community by which biochar had minor effects, or that the single-application was insufficient and a repeated application is necessary. Compost application on the other hand shifted the relative abundance of 16 bacterial families. In this study, the families of the Bacteroidetes and Chloroflexi were enriched and proteobacterial and acidobacterial families mostly declined.