Shallots (Best Option)
1/4 cup minced shallots per 1/4 cup minced onionShallots are closely related to onions and share many flavor compounds, particularly sulfur-containing compounds that give onions their characteristic taste. Their slightly sweeter and milder profile complements the bagel dough without overwhelming it. The moisture content is similar enough to maintain dough hydration balance.
When using shallots, finely mince and lightly sauté them to reduce moisture and mellow the flavor before incorporating into the dough. This prevents sogginess and ensures even flavor distribution.
Compared to onions, shallots produce a slightly sweeter and less sharp onion flavor in the final bagel, which can be more appealing to those sensitive to strong onion notes while preserving the traditional savory character.