Non-puddling rice cultivation would increase subsequent soybean yield. Soybean (cv. ‘Yukihomare’) was grown in farmers’ fields previously cultivated with puddled transplanted rice (Puddled Rice), non-puddled transplanted rice (Non-puddled Rice), and dry direct-seeded rice (Direct-seeded Rice) in central Hokkaido, Japan. Average soybean yield was significantly (p < 0.05) higher in Non-puddled Rice fields (411 g m−2) and in Direct-seeded Rice fields (404 g m−2) than in Puddled Rice fields (352 g m−2). The respective yield increases (16.8% and 14.7%) indicate that non-puddling rice cultivation increased subsequent soybean yield. The significantly higher values for shoot dry weight and number of seeds per m2 seen in fields after non-puddling rice cultivation suggest that non-optimal plant development during vegetative and early reproductive growth stages may be ameliorated. The increases in soybean yield seen in this study may encourage the adoption of non-puddling rice production under the rice–soybean rotation system in Japan.