Are you talking about onion seedheads (the flowers that form seeds)? If so, harvest the flower when most of the seeds are dry, then store in a cool, dry location for 2 or 3 weeks. You can store them for up to 1 to 2 years. Keep in mind that onions cross-pollinate readily, so the seeds will probably not be like to the parent plant unless the plants have been isolated. Also, the seeds of hybrids will not come true (they will vary in characteristics).
If you are talking about perennial Egyptian onions, they form a cluster of tiny bulbs, called sets, on top of the plant. They rarely form flowers. When the sets become heavy enough, the plant will bend over, and the sets will root in the soil. Thus, another name for this plant, Walking onion. Meanwhile, the onion bulb below ground will start to divide, forming 2 or more bulbs. To harvest the top sets, wait for the stalk to dry, which may occur in midsummer to fall; you can eat these or plant them for more onions. Once an onion bulb in the soil has divided, you can harvest some of the divisions in fall, but leave at least one bulb to continue on for next year. Or, you can leave these alone; they will produce, in a cluster, more stalks with topsets.
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