Soft rot is a bacterial disease that affects onions that receive too much water. Initial signs of a problem will be small soft spots along the bulb that are typically yellow in color. As disease worsens, a larger area across the bulb will soften and there will be a color change from yellow to brown. Once you have soft onion bulbs, there is nothing you can do to salvage them. You can, however, avoid the problem arising again by making a conscious effort to keep irrigation to a minimum while still giving the plant the amount of water it needs to develop. It is a good practice to water them just once a day, and then only enough to get the soil moist, not flooded.
Nematodes can be particularly problematic with onions. If you have nematodes in your garden, their feeding will turn your onion bulbs soft. You can identify nematodes as the source of this problem by the other types of damage they cause. The onion as a whole may become deformed or stunted during its development, and this will be visible especially in the leaves. Grayish scales may appear along the bulb as well. The best way to handle nematodes is to prevent them from ever cropping up by keeping your equipment and soil as clean as possible. You can also fumigate the planting area before you actually plant the onions.
A disease called white rot may be at the root of onion bulb softening. Along with the softening of the onion bulb itself, you may notice that leaves begin to wilt and finally die. There may also be a white fungus on the soil where the bulb meets the air. Rotating your onion crop between planting seasons and maintaining good sanitation habits with the soil and the equipment being used will decrease the chances of white rot infecting the onions. Once infection takes place, you will need to use a pesticide to get it under control.
Another primary cause of onion bulb softening is a disease called sour skin. Symptoms aside from the softening include soggy, decaying leaves and a sort of moldy circle running around the bulb from leaves that have already totally rotted. The bulb softening associated with sour skin is only at the bulb's top, or neck. Reducing irrigation, especially during hot, humid months, will help minimize chances of sour skin. Once an onion has sour skin, however, there is nothing you can do other than pull it and throw it away.