We hypothesized that cover cropping could increase soil microbial activities under various tillage systems and that increased microbial activities would improve soil properties. Soil sampling was conducted at two fields in Japan in 2009. At the Ibaraki field (Andosol, clay loam), three, tillage practices (no-tillage, plowing to 30 cm, and rotary tillage to 15 cm) and three types of winter cover cropping [bare fallow as control, hairy vetch (Vicia villosa Roth), and rye (Secale cereale L.)] were conducted from 2003 to 2009. At the Hokkaido field (Fluvisol, light clay), two tillage practices (autumn tillage and rotary tillage with a rotary tiller to a depth of 15 cm once in autumn and twice in a year, respectively), and four types of winter cover cropping (bare fallow, hairy vetch, bristle oat (Avena strigosa L.), and a mixture of hairy vetch and bristle oat) were conducted from 2006 to 2009. Soil microbial activities and the fungal-to-bacterial activity ratio (FIB ratio) were estimated by the substrate-induced respiration (SIR) method with the use of selective antibiotics. At the Ibaraki field, rye cover cropping showed higher microbial SIR than bare fallow at depths of 0-30 cm and rotary tillage maintained higher microbial SIR than no-tillage or plowing at depths of 7.5-1.5 cm. There was no meaningful interaction effect between cover cropping and tillage on microbial SIR. At the Hokkaido field, cover cropping and tillage had only limited effects on microbial SIR. High FIB ratios (indicating fungal dominance) were recorded with the use of cover crops in both fields. Fungal SIR, estimated from the microbial SIR and FIB ratio, was closely related to the content of total soil organic carbon (SOC) and the mean weight diameter (MWD) of water-stable aggregates. Based on SOC, fungal SIR was significantly higher under rye cover cropping. The relationship between fungal SIR and MWD was affected by tillage. We conclude that rye cover cropping and rotary tillage were very effective in increasing fungal SIR, SOC, and MWD in the Ibaraki soil. Field practices that enhance fungal activities might be effective in improving certain types of arable soil.