Combine yeast and warm water in a small bowl and stir until yeast dissolves. Stir in honey and let mixture stand until foamy, 5 to 10 minutes.

Meanwhile, oil a large bowl and set aside. Combine flours, salt, fennel seeds, and red pepper flakes in a large bowl. Pour yeast mixture into dry ingredients and stir. Mix dough with your hands, kneading a few times, until it’s a sticky, stiff, wet mass. Transfer to prepared bowl and cover with plastic wrap or a clean cloth. Place in a warm spot (such as oven with light on) and let sit for about 1 hour. Dough will rise and be a bit puffy, but it will not double in size as all-white flour doughs do.

Heat oven to 425°F and line 2 baking sheets with parchment paper.

Divide dough into quarters. Working in batches and keeping unused dough in bowl under a damp paper towel, roll out 1 piece of dough on a lightly floured surface until about 1⁄8-inch thick. Dough will be sticky and hard to work with, so don’t be afraid to use more flour.

Using a pastry cutter, cut out 3-inch circles. Use a smaller cutter to cut out a tiny circle in the middle of the circles to create a doughnut shape. Using a bench scraper or knife, carefully transfer rounds to prepared baking sheets. Poke surface of each round several times with a fork or skewer. Repeat with remaining dough.