Question: Can You Use Whole Wheat and White Flour Interchangeably?
By: Lindsay Van Nostrand
Published: March 2, 2010

I want to get into baking and am hoping to create healthier versions of my favorite treats. Can I simply substitute whole wheat flour for white flour with having to alter the recipe in any other way?

Answers:
Curt

Yes.
Chris Paulk

Yes, you can usually substitute most flours, I regularly substitute oat flour (from ground oats) for cookies and sometimes coconut or almond flours for more intense flavors in different baked goods.
Jenny Richards

That's not always the case, because you'll definitely get a texture and moisture impact if you do a straight 1:1 substitution. It's like subbing high-gluten flour for cake four - you wouldn't do that unless you knew what you were going to change in the recipe. Rarely will I do more than 50% whole wheat for a straight AP flour recipe. 
It really does depend on what you're baking and how delicate the crumb is supposed to be. In quick breads (like banana nut or zucchini), this is fine. The texture is deep enough that you can hide WW flour. But in something like a cake, I'd be reluctant (myself) to do more than 50% WW, and even then I would balance it out with cake flour instead of straight AP. You just have to be aware of the texture changes, and the fact that WW flour will absorb more liquid than AP flour, so you will come out with a denser dough. 
I sub WW in pizza dough at about 75% and it's considerably more chewy than a straight AP (or bread) flour dough, and the existence of the whole wheat germ in the flour means that it doesn't crisp the same way as AP flour. 
My .02.
Beverley Ann D'Cruz

Like purplehousedirt mentions above - not always. I also find using whole wheat flour gives items like bread and cake a denser quality so it could completely change the final outcome.
However, some cooks have found that using 'whole wheat pastry flour' can help lighten the texture of baked goods.
Scott Koeneman

Consider using whole wheat pastry flower if you are doing a 1-1 substitution. It is more finely ground then regular whole wheat flour and will give a texture similar to white flour. However, I have found it requires more liquid, so be prepared to go beyond what a white flour recipe calls for.