Tips For Growing Shallots That Are Disease And Pest Free

Bunches of shallows growing in the soil
(Image credit: JohnatAPW)

Cultivated for their mild and delicate flavor, shallots are the gourmet crop of the onion family. They can be used interchangeably with regular onions in most recipes, and growing shallots in your home garden is very doable. Many gardeners wonder, “Are shallots easy to grow, or is this specialty crop plagued with diseases, pests and other growing issues?”

What Are Shallots

If you've seen shallots at your local market, you've likely noticed their resemblance to small onions. Yet unlike regular onions which produce one large bulb, each shallot plant grows a cluster of teardrop-shaped onions. For this reason, shallots are sometimes called multiplier onions.


As a member of the allium genus, shallots have the same basic growing requirements and cultivation issues as regular onions. Shallots enjoy full sun and a loose growing medium. A moderate amount of water keeps them healthy, but too much soil moisture can lead to root rot. Although shallots produce small bulbs, they require approximately 90 days to fully mature.

Like regular onions, this allium crop is easy to grow in the home garden. Shallot diseases are rare, but other cultivation issues can occur. Here's what to watch for when growing shallots in a home garden:

Onion Maggots

Like the name suggests, onion maggots are the larvae of small housefly-like insects. The cream-colored larvae are about .25 inches (.6 cm.) long with a ridged body that tapers toward the head. Onion maggots feed on shallots and cause severe damage as they tunnel inside the bulbs.

Prevention is the best method for controlling onion maggots. These pests overwinter in the soil as pupae before morphing into adult flies in late spring. After mating, the female lays between 50 and 200 eggs at the base of host plants. The larvae burrow into the soil and begin feeding on the roots and bulbs. Multiple generations of onion maggots can hatch each year.

The adult flies are drawn toward decaying organic matter, including both animal and green manure. In addition to not adding these materials to gardens troubled by onion maggots, it's also advisable to clean all vegetable plant debris from the garden in the fall.

Row covers are also useful for preventing the adults flies from reaching the soil surrounding the shallot plants. This barrier method of pest control must be combined with a crop rotation schedule, otherwise the adult flies can emerge inside the row covers in the spring.

Bolting Shallots

Like onions, shallots are a biennial and are programmed to flower when exposed to cold temperatures following a warm spell. To prevent this, plant fall crops late in the year and spring crops after warm temperatures are here to stay.

As shallot onion sets have already grown once, they are more likely to bolt than plants started from seeds. Planting shallot onion sets smaller than an inch (2.5 cm.) in size can reduce bolting. If you start your shallots from seeds, it's advisable to transplant them when they are less than 6 inches (15 cm.) tall. Additionally, avoid heat and water stress as this can also trigger biennials to bolt.

If your shallots do bolt, immediately clip or break off the flowering stem. Otherwise, the stems will enlarge and thicken inside the bulb, which vastly shortens storage life. Bolted shallots can still be harvested. It's best to consume them within a few days or chop and freeze bolted shallots for future use.

Black Mold on Shallots

Finding black mold (Aspergillus niger) on shallots in storage is not uncommon. Surface mold can be washed off the bulbs and consumed by those not allergic or susceptible to this fungus. Heavily molded shallots are not safe to eat and should be discarded.

To prevent mold on shallots, handle the bulbs gently when harvesting to prevent damage. Injuries give the mold spores entry to the inside of the onion. To prevent surface mold from forming, properly cure harvested shallots and store the bulbs below 59 degrees F. (15 C.). Bear in mind, moving cold shallot bulbs to a warm environment can cause condensation to form on the onion's surface and lead to mold formation.

Laura Miller

Laura Miller has been gardening all her life. Holding a degree in Biology, Nutrition, and Agriculture, Laura's area of expertise is vegetables, herbs, and all things edible. She lives in Ohio.