Digestates are commonly used as organic inputs in agriculture. This study aimed to answer four questions: (1) What are the immediate and longer-term impacts of digestates on soil microbial activity?; (2) How much of the digestates’ carbon is mineralized within the first months? (3) How do the nitrogen, lignin, cellulose, and hemicellulose contents of digestates influence microbial activity and carbon mineralization? (4) How does the soil type influence mineralization? To investigate this, dehydrogenase activity (DHA) was measured in a field trial and in laboratory experiments with five digestates (DGs), cattle slurry, and cattle manure. DHA measurements were supplemented with soil respiration experiments using two different soils. DHA was significantly increased by all organic inputs, but decreased back to the control level within seven months under field conditions. Twenty percent to 44% of the organic carbon (Corg) in the digestates was converted to CO2 after 178 days. Soil respiration was significantly negatively correlated to lignin content (r = −0.82, p < 0.01) and not correlated to nitrogen, cellulose, or hemicellulose content. On the basis of equal carbon application, slurry promoted soil respiration and DHA more strongly than digestates in the short term.