Saving Onion and Shallot Seeds

Learn how to save seeds from onions and shallots.

sprouted onion

Many onions break dormancy and sprout during winter storage, but as long as they do not show signs of rot, these sprouted bulbs can still be planted out in early spring for seed production.

Photo courtesy Seed Savers Exchange

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The Seed Garden (Seed Savers Exchange, 2015) by Micaela Colley & Jared Zystro and edited by Lee Buttala & Shanyn Siegel brings together decades of research and hands-on experience to teach both novice gardeners and seasoned horticulturists how to save the seeds of their favorite vegetable varieties.

You can purchase this book from the MOTHER EARTH NEWS store: The Seed Garden.

Although common onions are biennial, they may still be an appropriate seed crop for beginner seed savers, provided a gardener takes care in choosing which varieties to grow. The vernalization requirement of common onions is easily fulfilled, and although sweet onions may present some storage challenges, overwintering storage onions is relatively straightforward. Saving onion seeds requires only slightly more time and work than cultivating seeds of many annual crops, which is fortunate given that onion seeds are notoriously short-lived, often remaining viable for just one or two years. Perennial members of the species, such as shallots and multiplier onions, are typically propagated vegetatively.

Crop Types

Allium cepa consists of three garden crops: common onions, shallots, and multiplier onions.

Common onions are categorized by color, pungency, shape, day-length requirements, and maturity. Bulb skins may be white, yellow, brown, red, or purple, and the bulbs themselves can be white or reddish purple. Onions are often categorized as sweet or mild (such as Vidalia or Bermuda types), or pungent (such as white and Spanish types). Bulbs vary from simple globes to more flattened shapes; they can even have the form of a spindle or toy top. Some onion cultivars are suitable only for short-term storage, while others were developed to store through the winter.

Shallots are a perennial form of Allium cepa that were once propagated almost exclusively through asexual reproduction. While shallot seeds are now available in garden catalogs, most commercially available shallot seeds are hybrid varieties and are therefore not suitable for seed saving.

Multiplier onion is a name generally applied to certain other types of perennial onions that are primarily reproduced vegetatively. Within Allium cepa, the main types of multiplier onions are potato onions (bulbing types) and walking onions (top-setting types). Seed savers commonly exchange these crops by sharing bulbs and topsets.

Green onion, scallion, and bunching onion are common names that do not relate to a particular species of Allium. Some scallions are produced from cultivars of Allium cepa that are harvested before the bulbs begin to develop or while the bulbs are still small. Other scallions, including the common variety ‘Evergreen Hardy White’, belong to the species Allium fistulosum and do not form bulbs at all.


The origins of Allium cepa are uncertain. The best evidence indicates that Allium cepa was domesticated from a wild species in the Middle East at least 5,000 years ago. By 2500 BCE, onions were being cultivated in Egypt. Onions were brought to India by 600 CE, to Europe by 900, to Russia by 1300, and to the Americas by 1500.

Growing Common Onions for Seeds

Some plants flower in response to photoperiod; onion plants bulb in response to photoperiod. Technically, all common onions are long-day plants—bulbing is initiated when day length reaches or surpasses a critical photoperiod. However, within this long-day species exist vari­eties that, confusingly, are classified as short-day, intermediate-day, or long-day types. Short-day onions generally require at least 10-hour days to begin bulb development; intermediate-day onions require days between 12 and 14 hours long; and long-day types have a critical photope­riod of 14 or more hours. In the United States, short-day onions are typically grown in the South, and long-day onions are grown in the North.

Common onions are biennial, forming a bulb in their first year of growth, then flowering and producing seeds—provided their vernal­ization requirement has been met—in their second season. Onions generally require expo­sure to temperatures below 54°F (12°C) for 8 to 10 weeks before they enter their reproductive phase; however, temperatures between 48 and 54°F (9 and 12°C) are optimal for vernalization. Vernalization can occur below this range, but onions in the ground are prone to rot in moist soil when the soil temperature is below 45°F (7°C). In drier conditions, bulbs may survive temperatures of 20°F (-7°C) or lower, depending on the variety. In cold climates, onions are often dug in the fall and stored in mesh bags or crates in a dry, well-ventilated location, ideally with a relative humidity of 60 to 75 percent. Optimal temperatures for vernalizing onions in storage are between 32 and 40°F (0 and 4°C).

Growing onions for seed begins by cultivating onions as if they were being grown for eating. At the end of the season, when the onion tops have fallen over, the bulbs are harvested and allowed to cure (if vernalizing in storage) in a warm, well-ventilated location out of direct sun until the tops, necks, and skins have fully dried. The dormant bulbs can then be stored until spring, though success with this process varies by cultivar. Storage onions and varieties that do well in long-term storage are easy to vernalize in this manner. Some onions may break dormancy and sprout during the storage period, but they can still be planted out for seed provided they are healthy. In the spring, when soil temperature is above 55°F (13°C), onions can be set out in the garden with 6 inches (15 cm) between plants in rows 36 inches (91 cm) apart, or spaced at least 15 inches (38 cm) on center.

Even where mild climates permit in-ground vernalization, it is still a good practice to lift onions. Lifting allows for a visual assessment of bulb traits and health, and also provides an opportunity to increase spacing between plants before they begin flowering. This is best done in spring, after vernalization, as onions that are lifted and replanted in fall often have a hard time re-establishing in cold soils.

Flowering, Pollination, and Seed Set

After vernalization, each onion plant sends up one or several leafless flower stalks called scapes—the inflorescence is initially enclosed within a large bract called a spathe. Onions bear hundreds of small white perfect flowers held in spherical umbels. Each perfect flower is protandrous—pollen is shed before the stigma becomes receptive—and onions rely on insects, including honey bees, syrphid flies, halictid bees, and drone flies, for pollina­tion. Flower stalks may grow to more than 3 feet (91 cm) tall, and staking will prevent lodging.

Variety Maintenance

In the garden, onion varieties should be isolated by 800 feet to half a mile (244 to 805 m). Gardeners who exchange seeds with others or who garden in settings that do not provide many landscape barriers may choose to use the upper end of this range as a starting point when determining an isola­tion distance. Commercial seed growers separate large plantings of different varieties by 1 to 2 miles (1.6 to 3.2 km). These isolation distances may seem daunting, but onions being grown for seed need to be isolated only in their second season, and only from other cross-compatible varieties that have also been vernalized and will therefore be flowering at the same time. Because of this, many gardeners can grow one variety of onion to seed each season. Multiplier onions, shallots, and common onions can cross-pollinate if they flower at the same time.

When a sufficient isolation distance cannot be provided, isolation cages can be used; polli­nators such as honey bees, blue bottle flies, and houseflies must be released into the cages.

Although onions are self-compatible, growing a large population helps to ensure a successful seed set and to conserve genetic diversity within a variety. Viable seeds can be obtained by growing 5 plants or fewer, though 20 to 50 plants is the recommended population size for seed saving. The upper end of this range helps prevent inbreeding depression and is preferable if a gardener’s intent is to save seeds for multiple generations or to share seeds with others. For those saving seeds for genetic preservation, a population size of at least 80 plants is recom­mended. Some loss can be expected from rot or disease during overwintering, so gardeners may want to grow more plants than the desired population size.

When roguing or selecting onions, seed savers should consider traits such as bulb color and shape.

Seed Maturity and Harvest

Onion seeds typically mature about 45 days after pollination. The seeds develop inside small fruits called capsules, which are pale green during development but fade as they dry. Each onion capsule has three chambers, and at seed matu­rity the capsule splits open at the top, exposing the black seeds contained inside. Although each onion flower has six ovules, and thus the potential to produce six seeds, only three or four mature seeds typically form in each capsule. The capsules located at the top of the seed head open first. Harvesting can occur any time after capsules begin to dehisce, and it may be best to harvest early in wet climates. If the plants are healthy and the weather is dry, it is ideal to harvest umbels when at least 20 percent of their capsules have split open.

Onion seeds can be harvested by cutting the scapes about 6 to 8 inches (15 to 20 cm) below the seed heads and placing the harvested material in an open container or bag. The umbels should be allowed to continue drying in a protected, well-ventilated space for 7 to 14 days; the cap­sules will continue to shatter as they dry.

Cleaning and Storage

Onion seeds can be threshed by gently rubbing the capsules between one’s hands or against a screen. Onion seeds are delicate compared to many other seeds; rubbing too aggressively can damage their thin seed coats.

After threshing, seeds should be screened and winnowed. At times, it can be hard to separate onion seeds from chaff, and floating (p. 85) is an alternative method of cleaning the seed lot. Immediately after floating, spread the seeds in a thin layer on screens to dry. Fans can be used to expedite the drying process, if desired.

When stored under cool, dry conditions, onion seeds can be expected to remain viable for two years.

onion seeds

Allium cepa

FAMILY: Amaryllidaceae

LIFE CYCLE: Biennial or perennial

SUGGESTED SPACING: When growing onions for seed, increase spacing to 6 inches (15 cm) between plants in rows 36 inches (91 cm) apart, or to at least 15 inches (38 cm) on center. Staking is recommended.

OTHER REQUIREMENTS: Onions are long-day plants; varieties should be selected for growing based on day length. Onions also require a vernalization period of temperatures below 54°F (12°C) for 8–10 weeks in order to flower and set seeds.

FLOWER TYPE: Perfect, self-fertile flowers are protandrous and shed pollen prior to stigma receptivity. Clusters of flowers are held in spherical umbels.

POLLINATION: Insect-pollinated

MATING SYSTEM: Mixed. Protandry facilitates cross-polli­nation. However, onions self-pollinate when insects transfer pollen between flowers on the same plant.


FRUIT TYPE: Dry, dehiscent fruit (capsule)

SEED MATURITY: Seed maturity occurs in the second growing season, when capsules split open to expose mature black seeds. Shattering is common.

SCREEN SIZE: 4⁄64–9⁄64 inch (1.5–3.5 mm)


ISOLATION DISTANCE: 800 feet–1⁄2 mile (244–805 m)

Population Size

For Viable Seeds: 5 plants

For Variety Maintenance: 20–50 plants

For Genetic Preservation: 80 plants

For more on seed saving, see our Seed Saving Guide.

Reprinted with permission from The Seed Garden, by Micaela Colley & Jared Zystro, edited by Lee Buttala & Shanyn Siegel and published by Seed Savers Exchange, 2015. Buy this book from our store: The Seed Garden.