It's common knowledge that bread made with whole wheat flour is much healthier than if made with refined flour, and it's a misconception that whole wheat bread be heavy and sodden. But expecting a homemade loaf of whole wheat bread to resemble a soft and squishy supermarket loaf is unrealistic; they are two entirely different breads. Plastic-wrapped supermarket breads have paragraph-long ingredient lists—dough  conditioners, additives, and a litany of unrecognizable words—but a loaf you make at home can have as little as four ingredients. This said, it is possible to make a really good loaf of whole wheat bread in your home kitchen if you follow a few simple but key steps. All the same procedures apply as if making any other yeast-leavened bread, but there are a couple more which are essential when using 100% whole wheat flour.

The first of the two is incorporating a preferment into the dough. This is a method that can be applied to any yeast dough and is one that is often used by professional bakers. A preferment is nothing more than combining a portion of the flour with some or all of the water and a bit of yeast...hence it's name, it is a per-fermentation. Other common names for this are: starter, mother, sponge, poolish, leavain, and biga. The preferment in these recipes is a biga; Italian in origin it has a low moisture content and resembles a small ball of dough, rather than a batter or slurry like some of the other preferments. Though simple to make, preferments offer the dough many positive attributes, such as superior dough structure, complex flavor, and better keeping quality.

The other method, which is truly essential to whole wheat bread making, is called autolyse, and translates loosely and somewhat blatantly as “self-destruction” or “self-digestion,” referring natural enzyme actions that take place when liquid and flour come into contact. Autolyse is a very simple method of soaking flour with water—essentially making a dough with no yeast or salt—which allows the strands of gluten to relax, soften, and absorb moisture, thus strengthening them as the dough is kneaded and allowing the bread to have more rising power; this simple but paradigmatic method was invented by famed French baker, Raymond Calvel (1930-2005).

The reasons these methods are so important to making really good whole wheat bread is because of the flour itself. The difference between whole wheat flour and white flour is that whole wheat flour is simply wheat berries that are ground—the whole berry, hence it's name, which includes bran, germ, and endosperm—whereas white flour is only ground endosperm. Removing the bran and germ excludes most of the fiber and nutrients from the flour  (this is why white flour is “enriched), but it also presents a few differences for the baker. The endosperm is where most of the protein or gluten in the wheat berry is found, so white flour naturally has a higher gluten content, which is good for bread making. But the real crux relates to the bran, or the outer shell of the berry. The bran in whole wheat flour absorbs more liquid than a recipe made with white flour (and a under-hydrated dough will surly be a heavy one), but it's even more than that. If not softened properly, the bran can act like tiny knives and cut at the gluten strands as the dough is kneaded, reducing it's rising capacity greatly. This is where autolyse comes in. By soaking the flour you are not only beginning the natural enzymatic process of swelling, aligning, and strengthening the gluten strands, you are also softening the bran and creating more elasticity in the dough.

While this may sound complicated it's really not, it's actually quite simple. The process goes something like this: Place two bowls side-by-side. In one bowl mix a portion of the flour and water together just until it's moist; you don't want to knead it at this point. In another bowl mix together a smaller portion of the flour and water, only this time you add a bit of yeast. Cover the bowls and allow them to rest for 30-90 minutes. Next, combine the contents of the bowls along with a bit more yeast, a little salt, and some honey and olive oil if you like. If kneading the dough mechanically use an upright mixer fitted with a dough hook and knead it on medium speed for about 8 minutes; kneading by hand may take twice that long (and strengthens your arms as well as the gluten). Place the dough into a bowl and allow  it to ferment and rise for about an hour, maybe a little longer depending on the temperature. After it has risen, gently shape it into loaves again and allow for a second rise in the pans. Lastly bake the loaves in a preheated oven.

Keep in mind that bread basically makes itself, you simply provide the proper conditions and guide it along. Some of your breads may be mediocre—some may be downright flops—but many will be truly incredible and worthy of praise and marvel. Whole wheat bread is exceedingly good for you, and it makes the entire house smell great while baking. The tangy, nutty flavor from whole wheat bread is unsurpassed; even the mediocre loaves will be better than a squishy supermarket product...and it's something you'll have made with your own hands. Like anything, the more you make bread the easier it becomes. Bake your own bread, you'll be glad you did.
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100% Whole Wheat Bread
Makes 2 loaves​
2 cups whole wheat flour

1 cup water

2 teaspoons instant yeast

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4 cups whole wheat flour

1 3/4 cups water

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1/4 cup honey

1/4 cup olive oil

3 teaspoons instant yeast

3 teaspoons kosher salt

In one bowl make a preferment by combining 2 cups of whole wheat flour with 2/3 cups water and 2 teaspoons of instant yeast.  Begin the autolyse in another bowl by combining 4 cups of whole wheat flour and 1 ½ cups water. Stir each bowl just enough to combine the ingredients, taking care not to get yeast into the bowl with the autolyse. If the contents in either of the bowls need more water, add a small amount. Cover both bowls and allow to rest and ferment for 30-90 minutes, during which time the preferment will begin it's job multiplying yeast and fermenting flour, and the autolyse will soak the grain, swelling the gluten.
After an hour or so, combine the ingredients from both bowls into the bowl of an upright mixer fitted with a dough hook. Add the honey, olive oil, salt, and 3 teaspoons of yeast (add the yeast and salt on opposite sides of the bowl). Knead the dough on medium speed for  about 8 minutes.
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Place the dough in a lightly oiled container, cover it loosely, and allow to ferment for 1-2 hours, or until doubled in bulk. Deflate the dough and allow it to ferment an additional 30 minutes.

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Turn the dough out onto a floured work surface and cut it into 2 or 3 pieces. Shape into loaves and place into lightly oiled pans. Loosely cover the loaves with plastic wrap and allow to ferment for 30-60 minutes, or until double in size and when gently touched with a fingertip an indentation remains.
Bake the breads for about 30-40 minutes, adding steam to the oven a few times (either with ice cubes or a spray bottle) and rotating the breads every ten minutes. The breads are done when they are dark brown and sound hollow when tapped upon. Remove the breads from their pans and allow them to cook on a wire rack for at least 10 minutes before slicing.
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Whole Wheat Brown Rice Bread
Makes  2 or 3 loaves​
1 cup brown rice

3 quarts water

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cooked rice

2/3 cup cooking liquid

2 cups whole wheat flour

2 teaspoons instant yeast

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4 cups whole wheat flour

1 3/4 cups cooking liquid

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1/4 cup honey

1/4 cup olive oil

3 teaspoons instant yeast

3 teaspoons kosher salt

Combine the rice and water in a medium pot and bring to a boil; lower the heat to simmer and cook the rice for about 45 minutes or until very soft. As the rice cooks add more water to the pot as necessary because the cooking liquid, which is full of nutrients, will become part of the recipe. After the rice  is cooked allow it to cool in the liquid to room temperature, refrigerating if necessary. After the rice is cooled drain it, squeezing it with your hands or the back of a spoon, reserving the cooking liquid.

Place two bowls side-by-side; one will hold the pre-ferment, the other autolyse. In one bowl combine the cooked and drained rice with 2/3 cup of the cooking liquid, 2 cups whole wheat flour, and 2 teaspoons instant yeast. Stir it just until combined then cover it with plastic wrap. In the other bowl combine 4 cups whole wheat flour and 1 1/3 cups cooking liquid; stir it just until combined then cover it with plastic wrap (take care not to get yeast into this bowl). Allow the bowls to rest at room temperature for about an hour, during which time the preferment will begin it's job multiplying yeast and fermenting flour, and the autolyse will soak the grain, swelling the gluten.

After an hour or so, combine the ingredients from both bowls into the bowl of an upright mixer fitted with a dough hook. Add the honey, olive oil, salt, and 3 teaspoons of yeast (add the yeast and salt on opposite sides of the bowl). Knead the dough on medium speed for  about 8 minutes. Place the dough in a lightly oiled container, cover it loosely, and allow to ferment for 1-2 hours, or until doubled in bulk. Deflate the dough and allow it to ferment an additional 30 minutes.
 

Turn the dough out onto a floured work surface and cut it into 2 or 3 pieces. Shape into loaves and place into lightly oiled pans. Loosely cover the loaves with plastic wrap and allow to ferment for 30-60 minutes, or until double in size and when gently touched with a fingertip an indentation remains.

Bake the breads for about 30-40 minutes, adding steam to the oven a few times (either with ice cubes or a spray bottle) and rotating the breads every ten minutes. The breads are done when they are dark brown and sound hollow when tapped upon. Remove the breads from their pans and allow them to cook on a wire rack for at least 10 minutes before slicing.