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When shallots are growing, they send up scapes the same way garlic and other onions do. Small mammals love chewing on these. You can protect the shallots by covering the garden with fleece or a net, which will keep predators out.  The netting isn't necessary until spring, when the shallots will start to actively grow. You can also protect the shallots from worms by sprinkling the area with wood ashes every couple months. Shallots don’t like competing with weeds, so it’s important to stay on top of removing them from the soil where shallots are growing.  Just be careful that you don’t accidentally pull out the shallot scapes when you're weeding or removing grass.  Weed the area by hand, rather than with a spade or other tool, to prevent damaging the roots. You won’t have to water your shallots much, even during the active growth phase, because shallots don’t require a lot of extra water. However, if the weather turns dry and you don’t get much rain, make sure the soil stays somewhat moist. If your shallots begin to flower, this will take energy away from the bulbs, meaning your onions won’t be as large or tasty. To prevent this from happening, cut off any flowers that start to grow. Cut flowers at the stem to prevent the shallots from going into reproduction mode.
Protect them from pests and predators. Weed the area regularly. Water the plants during dry spells. Cut off flowers.