In a medium bowl, whisk together whole wheat flour, yeast and warm water until well combined. Let sit for 10 minutes until slightly foamy.

Meanwhile, in a large bowl or in the bowl of a stand mixer, whisk rye flour, cocoa powder, caraway seeds, instant espresso and salt until combined. Pour in molasses, oil and yeast mixture. Stir until just combined. Add bread flour and stir just until dough forms.

Knead dough by hand on lightly floured surface 10 to 15 minutes, adding just enough extra bread flour as needed until smooth, soft, elastic and only slightly sticky dough forms; OR, use the dough hook attachment to knead dough in stand mixer for 5 minutes medium low speed, adding just enough extra bread flour as needed until smooth, soft, elastic and only slightly sticky dough forms (it should pull away from sides of bowl).

Shape dough into a ball and transfer to a lightly oiled large bowl. Turn once to coat. Cover bowl with plastic wrap and let dough rise 1 hour to 1 hour 30 minutes until doubled.

Meanwhile, heat the oven to 425 degrees F and line two baking sheets with parchment paper or silicone mat, or lightly grease with oil or cooking spray.

Punch down the dough to degas. Divide and shape into 12 equal-size pieces (about 3 ounces each in weight). Using your thumb and forefinger, poke a 1-inch hole in the center of the ball and gently stretch to form a hole. Place shaped bagels on the baking sheet and cover with a towel for 10 minutes.

Meanwhile, bring a large pot of water to boil. Reduce water to a simmer and place bagels in water one or two at a time. Cook for 30 seconds, then flip over with a slotted spoon and cook for another 30 seconds. Use the slotted spoon to carefully remove the bagels and set on a wire rack. Repeat with remaining bagels. Place bagels on the prepared baking sheets.

Bake bagels for 15 minutes until cooked through and lightly browned on bottom. Transfer to a cooling rack to cool completely.