Understanding the effects of soil amendments on organic matter dynamics is essential for the sustainable management of soil. Less is known about the effects of biochar in comparison to commonly used organic fertilizers on soil aggregation and organic matter dynamics. Here, we aimed to analyze the effect of biochar, slurry, and manure on carbon (C) mineralization and macro-aggregate formation. Soil material whose macro-aggregates (>250 mm) have been carefully crushed was mixed with biochar and/or slurry or manure and incubated at 5 C, 15 C, and 25 C over a period of eight weeks. We determined and modelled the CO2 emissions over the course of the incubation experiment and analyzed the contents of newly formed macro-aggregates, associated C and microbial biomass C after four and eight weeks. Temperature effects on the decomposition intensity were found to be highest for the manure and lowest for the biochar application. CO2 fluxes across treatments and temperatures were mostly satisfactorily described using 1- or 2-pool-models. Macro-aggregate yields were smaller at higher temperatures in the control and biochar (after 4 weeks) as well as manure (after 4 and 8 weeks) treatments, presumably because of a metabolization of binding agents. At 15 C, slurry addition resulted in significantly higher aggregate yields compared to all other treatments, which may be attributed to its more liquid state allowing an easier and more efficient contact with mineral particle surfaces. In combination with slurry, biochar resulted in lower aggregate yields than slurry alone at 15 C. Manure application did not significantly change aggregate yields compared to the control. Correlations between aggregate yields and the microbial biomass or CO2 production point towards a direct interaction of the respective substrates with soil particles to form aggregates followed by decomposition of the amendments and production of microbially derived aggregate binding agents.