Crop rotation in agriculture can lead to increased crop productivity in the rotation and improved soil fertility as a result of residue incorporation. Unfortunately, residue incorporation is not a common practice in crop production systems under the Mediterranean regime, largely due to the lack of information on the effect of the follow-up crops. Therefore, this study was conducted with six biannual rotations (bread wheat–canola, bread wheat–bean, durum wheat–canola, durum wheat–bean, corn–canola and corn–bean) using four residue incorporation levels (0, 50, 100 and 200%) in an Andisol in south central Chile. Grain yield and residue production were evaluated in the canola and bean crops 5 years after initiating crop rotation. The previous crop affected canola grain yield and residue production, which were both higher after corn. Meanwhile, the residue incorporation level had a slight effect on residue production after bread wheat. Only bean grain yield was affected by the previous crop, which was higher after the durum wheat and corn crops. The residue incorporation has marginally affected residue production after bread wheat. Finally, residue incorporation at different levels under the conditions of the present experiment had a minimal effect on bean and canola residue production following the bread wheat crop. The best crop rotation for canola grain yield was corn–canola, which produced 0.54 Mg/ha (18.3%) higher yield than the average of the other two rotations. The best crop rotation for achieving higher bean grain yield was corn–bean, which yielded 0.52 Mg/ha (12.3%) higher than the average of the other two rotations.