In a large bowl, combine the yeast, 1 tablespoon of malt, and the warm water. Allow yeast to proof until the surface becomes foamy (this will take around 5 minutes). Whisk in the salt. Add the whole wheat flour and 2 cups of the all-purpose flour, stirring with a wooden spoon until incorporated.

Place the bagel dough on a solid sturdy surface and slowly work in the rest of the all-purpose flour. Knead for 10 minutes or until smooth and elastic. Coat the dough with olive oil, place in a bowl, and cover tightly with a clean dish towel.

Allow to rise until the dough has doubled in volume; approximately 1 hour, depending on temperature and altitude. Time can vary significantly based on these factors.

After your vegan bagel dough has doubled, knead it lightly for 1 minute. Divide the dough into 12 equal parts. Roll each piece into log and then fold it into a circle, firmly pressing the seam together. Place each bagel on a lightly floured surface, cover with a clean towel, and let rise until doubled; about 1 hour.

Meanwhile, preheat your oven to 500 degrees F and place a baking stone inside, if using. Otherwise, the bagels can be baked on a standard sheet pan. In a large pot, bring 3 quarts of water to a boil and add the baking soda along with the remaining 3 tablespoons of malt. The baking soda is necessary to properly texture and brown the bagels.

After the bagels finish their second rise, boil each bagel for 1 minute on each side, keeping the water at a consistent, rapid boil.

Now your bagels are ready to bake. Top them with any desired seasonings, patting them gently into the top with your hands. Transfer carefully to your baking stone or sheet pan, and bake for about 15 minutes.