Field experiments were conducted to evaluate the effects of 4 rice farming systems (fallow, white clover (WC), rye and rye + WC) at 3 straw mulching levels (0, 500, 1000 g/m²) under no-till, direct-sown and unfertilised rice-based cropping systems in a temperate climate in Japan. From 1999 to 2001, white clover and rye were grown during winter (November–May) in Ehime Prefecture (33°57′N, 132°47′E, 15 m a.s.l.) to evaluate the effects on rice growth and yield-related characteristics. Seed germination was greatest in clover–rice cropping systems (60, 68%) followed by rye + WC–rice (56, 57%) for the 0 and 500 g/m² mulching treatment, respectively. Rice yielded 1.26–4.12 t/ha in 2000 and 0.54–3.80 t/ha in 2001. Panicle number ranged from 84 to 248 and 47 to 323/m² in 2000 and 2001, respectively. WC with light rice straw mulching in rotation with rice produced moderate rice yield in no-till, unfertilised, direct-sown rice-based cropping systems. Heavy mulching of rice straw in the WC and WC + rye is not recommended because it leads to a decrease in white clover biomass production. However, straw mulching in fallow–rice and rye–rice cropping systems is essential for improving seed germination and seedling establishment while providing nutrients to rice at later growth stages.