The use of plastic film imposes various environmental risks in agroecosystems. The replacement of plastics with organic materials for mulching has been suggested to enhance the sustainability of agroecosystems. However, whether woodchip mulch can be used for annual crops needs to be verified. We examined the effects of mulberry woodchip mulches on tomato-fruit yields over two successive years. Mulberry is the unique food plant of silkworms, and it will be better if its pruned shoots can be recycled rather than incinerated as waste. Setting three treatments, including woodchip mulch, weed-free and weedy (i.e., unweeded) treatments, we compared the amounts of fresh-marketable and unmarketable tomato fruits. The yields of fresh-marketable tomato fruits in the woodchip mulch treatment were significantly 16–57% higher than those in the weed-free treatment and comparable to those in the weedy treatment. The yields of unmarketable dehiscent tomato fruits in the weed-free treatment were significantly 46–86% higher than those of the other two treatments. The woodchip mulches extensively suppressed the weed density, while the grown weeds became large, preventing strong sunlight exposure and dehiscence of tomato fruits. Current results suggest that woodchips could be a possible alternative to plastics, facilitating climate change mitigation with agroforestry practices.