Though most people rely on commercial producers for their bread, baking one’s own at home is rather simple to do. Combined in a bowl with flour and water, dried yeast reacts marvelously, coming vigorously to life as it ferments sugars and creating a delicious balloon of gas-filled dough. Thirty minutes in the oven produces a house full of aromas and a hot, steaming loaf on the table. It’s easier, for sure, than pie. With white flour, anyway.

But using whole wheat takes things up a notch. Unlike white flour, whole wheat–like other unrefined grains–contains germ and bran. These two components bear minerals like zinc, magnesium and iron, as well as omega-3 fatty acids and dietary fiber. They also add a nutty array of flavors to a loaf of bread, as well as a fuller texture. Thing is, they also make life harder for bakers. For one thing, bran and germ soak up water, which can dry out a loaf and make it crumbly–and largely for this reason, bakers cannot simply substitute whole grain for white. Rather, recipes must be entirely recomposed. Germ and bran also add weight to the dough, which can impede its capacity to rise, leading to loaves almost as dense as French cobblestone. But a properly made whole wheat loaf can be surprisingly light as well as healthy to eat in ways that white bread isn’t, and if one loaf should fail, it’s worth it for the home baker to try again for that perfect honey-brown bread.

It helps to try a few basic methods. First and foremost, you must use enough water.

“Probably the most frequent mistake in baking whole wheat bread is not using enough water,” says Dave Miller, a whole wheat enthusiast and the owner of Miller’s Bakehouse near Chico, Calif. “You really need to hydrate the flour. Only then can you get really beautiful, soft bread.” White flour dough can be made with as little water as just 60 percent of the flour weight–a so-called “baker’s percentage” of 60 percent. But whole grain flour demands significantly more. Most commercial bakers use at least a 90-percent baker’s percentage of water–that is, 14.4 ounces to a pound of whole wheat flour. Miller uses even more water than that–often a 105-percent baker’s percentage. That means he uses almost 17 ounces of water to 16 ounces of flour.

And in San Rafael, Calif., Craig Ponsford, of the bakery Ponsford’s Place, goes even higher–up to 120 and even 130 percent water. “My dough is like soup when I first combine the flour and water,” says Ponsford, who makes breads and pastries with nothing but 100-percent whole grain flour. “Bread is all about the water. Water is what makes light, fluffy loaves, and in the case of whole wheat you need lots of water.”

You also don’t want to over-knead your whole wheat dough. That’s because it contains flakes of bran which can actually cut the dough like knives.

“Those will slice through the gluten strands when you’re kneading the dough,” says Jonathan Bethony-McDowell, a research baker in Washington State University’s Bread Lab, a facility used in national wheat breeding programs. This cutting action, he explains, will damage the consistency and structure of the dough and curtail its ability to rise. Anyway, an extra wet, gooey dough may be too sticky to easily knead, and a quick mix will do.

You’ll also probably have to give your whole wheat dough more time to rise than you would white dough, thanks to the heavy germ and bran particulates. But Ponsford warns that there is only so much time you can give. That is, at a certain point, a ball of dough will reach its maximum volume. Then, as the fermenting yeast continues metabolizing the sugars in the wheat, the dough stops rising and reverses. “If you let your dough over-ferment, then the gluten deteriorates, and the dough can collapse,” Ponsford explains.

So, what’s the sweet spot? The rule of thumb when using a baker’s percentage of 1 percent yeast (remember, that’s 1 percent of the flour weight) says you can let whole wheat dough rise for about three-and-a-half hours at 75 degrees Fahrenheit before it attains its maximum volume, according to Ponsford. But Ponsford usually uses one-tenth of a percent yeast. (A gram-sensitive scale would be helpful here.) Thus, the yeast takes longer to attain its full vigor–and the dough longer to reach its maximum gas capacity. Some of Ponsford’s whole wheat breads spend 36 hours rising, he says–a time span that he explains allows great development of flavor as the yeasts work on the germ, bran and endosperm. Ponsford likens these day-and-a-half breads to the great red wines of Bordeaux. Like a good Cabernet Sauvignon, he explains, such complex, long-fermented whole grain bread will last longer on the shelf and can be matched to stronger-tasting foods.

Beyond bread, those with a sweet tooth can also bake using whole grain flour. That’s what professional pastry chef Kim Boyce has been doing since 2007, after she discovered while experimenting with a recipe just how good whole wheat pancakes can be. Today, Boyce owns and operates Bakeshop, a pastry house in Northeast Portland, Ore. For Boyce, using whole grains is not about the health benefits. Rather, she believes they make better pastries, plain and simple.

“Whole grains give you a toothsome texture and a little nuttiness,” she says. “There is so much more flavor in whole grains, and that lets me pair my pastries with fruits and wines.” For cookie recipes, Boyce uses entirely whole grain flour, but for items that require some fluff, like scones and muffins, Boyce uses a 50-50 blend of white flour to whole grain flour.

Boyce says it doesn’t take a pro baker to replicate her recipes, many of which she has published in her 2010 cookbook, Good to the Grain. “People can totally do this at home,” Boyce says. For those hoping to try their own creations, Boyce advises starting with a favorite baking recipe that calls for white flour and substituting in a quarter or a half cup of whole grain flour in a one-to-one swap. Those who proceed further toward entirely whole wheat pastries must start boosting the liquid volumes, she advises, whether milk, water or cream, to accommodate the higher levels of water-grabbing germ and bran.

Whole wheat baking, clearly, takes some effort and time to do well. But whole grain proselytizers believe it’s well worth it–that the health benefits of eating whole grain flour, as well as the bonus of improved flavor, outweigh the challenges of turning it into bread. White flour, says Bethony-McDowell, at the WSU Bread Lab, is nothing but powdery white endosperm–almost entirely void of nutrition. “It’s just starch,” he says. “Ninety percent of the nutrients in whole wheat go out the door as soon as you mill it into white flour.” Monica Spiller is another advocate for whole grains–plus making them with sourdough yeast, which she and others say are good for the digestive tract. She sells heirloom seeds to farmers through her online nonprofit, the Whole Grain Connection, and she voices an increasingly supported notion that gluten intolerance is a misidentified condition.”I think gluten intolerance is actually an intolerance to refined flour,” she says. Ponsford, too, has observed this, he says, in customers at his bakery who once sometimes reported stomach aches after eating refined wheat products but who can digest his whole grain pastries and breads just fine.

The verdict may not be in yet on this health claim–but the jury, anyway, is baking good bread.Following are two recipes from the experts.

Dave Miller’s Basic Whole Wheat Bread

Ingredients:

16 ounces whole wheat flour

16.32 ounces water (102 percent of flour weight, though extra dry flour may call for 105 percent, or 16.8 ounces, of water)

3.2 ounces sourdough starter (or, for non-sourdough, 1 tsp activated dry yeast)

0.38 ounces salt

Directions:

Mix the flour with 90 percent of the water in a bowl. Let sit for 30 minutes–a lapse of time called the”autolease,” during which enzymes activate and convert starches into sugar. Next, mix the dough in an automatic mixer or by hand for several minutes. Add the remaining water, sourdough starter and salt. The dough will be very gooey–almost like batter. Allow it to sit for three hours in a bowl at room temperature. Next break apart the dough and shape into loaves. Allow 20 minutes of rising. Punch down the dough loaves and allow one more rise. After three hours, place in an oven preheated to 520 degrees F (yes–this is very hot). After 15 minutes, reduce the temperature to 470 for 20 minutes. For 15 more minutes, open the oven door a crack, which allows moisture to escape and facilitates crust formation. Remove the finished bread.

Monica Spiller’s Sourdough Starter

Ingredients:

1/2 cup water

1/2 cup whole wheat flour

Directions: Combine half the flour and half the water in a glass jar and cover with a cloth. Stir two times per day. After about three days, the mixture should be bubbling. Using ph paper, measure the acidity. Monica Spiller suggests aiming for a ph of 3.5. Now, feed the starter half of the remaining flour and water. The ph should hit 3.5 again in slightly less time–two days, perhaps. When it does, add the remaining flour and water. This time, the increasingly vigorous starter will hit the desired ph in just eight hours. It is now ready to begin using. Always leave a portion in the jar to allow indefinite propagation. Maintaining the starter is easy. You must only remove about half of its volume every week, either to discard or (preferably) use in bread, and “feed” the starter with fresh whole wheat flour and water. If you bake less frequently, keep the starter in the fridge. Keep it covered with a cloth.