A short-term incubation study was carried out to investigate the effects of different biochar (pyrochar and hydrochar) amendments on soil properties. Pyrochars and hydrochars derived from sewage sludge (PSS and HSS), poultry manure (PPM and HPM), and olive oil solid waste (POW and HOW) through slow pyrolysis and hydrothermal carbonization (HTC) were mixed with soil in three different doses (1, 2, and 4%) and subjected to a 120 day incubation period. Selected soil physical (water-stable aggregate [WSA]) and chemical (pH, EC [Electrical conductivity], CaCO3, total N, soil organic matter [SOM], C:N ratio, and available P) were investigated at the end of incubation, while soil biological properties (urease [UR], alkaline phosphatase [ALP] and β-glucosidase [βG] enzyme activities) were evaluated in a time-course sampling, at 1, 60, and 120 days of the incubation. The results generally indicated that total N and soil available P contents were more responsive to pyrochars and hydrochars produced from different biomass wastes. All pyrochars showed significantly higher total N and available P over hydrochars depending on the application doses and only HOW showed a prominent enhancement in SOM over POW. In general, soil ALP activity did not show distinct changes in pyrochar amended conditions, whereas it seemed to increase significantly by the amendments of hydrochars, especially HSS (p < 0.05), over the control and application dose. The βG activity displayed a similar pattern with that of ALP activity in that increasing additions of hydrochars produced from all three waste biomasses significantly stimulated (p < 0.05) βG activity over those of their corresponding pyrochars. Unlike from ALP and βG activities, UR tended to decrease significantly (p < 0.05) in all pyrochar added treatments but depending on the waste biomass type and application dose; it showed different change patterns under hydrochar treatments. Overall, the results showed that the hydrochar obtained from HTC is more effective on the biological properties of soil compared to the biochar obtained by pyrolysis. On the other hand, it is possible to conclude that pyrochar was a very stable and recalcitrant C source than hydrochar according to microbial activities and could be an efficient, long-term strategy to sequester C in soils.