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Baking with Whole Wheat Flour (and Lemon Raspberry Thumbprint Cookie Recipe)

 Written by contributor Stacy Karen of A Delightful Home

The holiday season often finds us in the kitchen baking treats or at gatherings eating treats!

One way to take the load down is to replace ingredients with whole food alternatives. For example, substituting butter in place of margarine, exchanging canola oil for the healthier coconut oil, and including natural sweeteners whenever possible are all excellent methods for making sweets a little healthier.

Trading bleached, white flour for whole wheat is another recipe tweak that will bring some extra nourishment to desserts and snacks.

Baking with whole wheat flour is not always straight forward, but it is worth adjusting frequently-used recipes in order to make them more healthful.

The Benefits of Whole Wheat Flour

Whole wheat flour contains nutrients and fiber that are not present in bleached, white flour; namely bran and germ. White flour has a high glycemic index, can cause elevated blood sugar levels, and is basically devoid of any nutritional value.

On the other hand, whole wheat flour is a nutrient dense food.  Cynthia Lair explains it well in her book, Feeding the Whole Family:

“For daily consumption whole grains are superior to refined grains because the whole product contains protein, fiber, B vitamins, calcium, iron, vitamin E, and life (the germ of the grain is the live part).”

Types of Whole Wheat Flour:

Pre-packaged Whole Wheat Flour
Flour labeled “whole wheat” at your local grocery store is most often made from red wheat berries. It has a strong wheaty flavor. I find that many brands have a stale taste, however, King Arthur Flour is said to be much fresher. So you might want to give that a try, if it’s available.

Your local health food store probably has a few different options such as whole wheat pastry flour. If purchasing from bulk bins, be sure to choose a store than has a high turnover rate, so the flour is as fresh as possible.

Hard Red Wheat

Hard red wheat has a strong wheat flavor and is well-suited to yeast breads. It gives a dark color to baked goods.

Hard White Wheat
Hard white wheat is milder in flavor than hard red wheat. It is an excellent choice for those beginning to use whole grain flours since its mild flavor is often well accepted by the entire family.

Flour made from hard white wheat is an excellent choice for bread and pizza crusts.

Soft White Wheat
Soft white wheat makes a delicious pastry flour that is excellent for baking quick breads, muffins, pancakes, scones and cookies. Whole wheat pastry flour does not work well in yeast breads.

The gluten content in soft wheat  is very similar to white flour, making it easy to use as a substitution.  It has a finer texture than flour made from hard wheat.

Sprouted Wheat
Sprouting wheat improves nutritional value and makes the grain easier to digest. Similar benefits can be produced through soaking flour, however, sprouting is more convenient and enables us to fulfill a cookie craving in a reasonable time frame rather than waiting a few hours (or even over night) for flour to soak.

I”m not an expert in the soaking and sprouting process, so if you”d like to know more, I encourage you to download Katie”s free e-book, Is Your Flour Wet?, and check out this post at Modern Alternative Mama: Tips for Baking with Spouted Grains

Should I grind my own wheat?

I’m afraid to say that freshly ground flour is best, because it may seem to complicate things, but honestly, it is best! Freshly ground flour contains more vitamins and minerals than flour that has been sitting for weeks or months. It also tastes much better than pre-packaged. I mean, much better.

Another benefit: It  is cost effective to grind your own wheat (once you get past the purchase of a grain mill). If you to learn more, read this explanation from Laura at about how she .

How to Substitute White Flour With Whole Wheat Flour

When first adapting a recipe, it is wise to start by replacing half of the white flour with whole wheat. This is usually a safe way to go and results are often very good.  Even with this small adjustment, your baked goods will have more nutritional value (and you’ll feel better serving them).

If you are satisfied, leave it there. If not, then gradually increase the amount of whole wheat each time you make the recipe. Or, get brave and try replacing all of the white flour for whole wheat and see what happens! (I often do this because I am impatient.) It”s fairly safe to do this when baking muffins and quick breads.

Whole wheat flour absorbs more liquid than all-purpose flour, so you may need to increase the liquid content a little (by a few tablespoons) or decrease the amount of flour.

Are you ready to try a yummy whole wheat cookie now?

The following recipe is a nutritious take on traditional thumbprint cookies; they have a light sweet flavor with a nutty undertone. My family loves these cookies, I hope yours will, too.

Lemon Raspberry Thumbprint Cookies

Recipe adapted from Feeding the Whole Family by Cynthia Lair

Makes about 24 cookies.


2 cups whole wheat pastry flour
1 cup almonds, ground into fine meal
2 teaspoons baking powder
1 tablespoon lemon zest
½ teaspoon sea salt
10 tablespoons unsalted butter, melted
½ cup maple syrup
2 teaspoons almond extract
½ teaspoon lemon extract
Raspberry preserves


Preheat oven to 350 degrees F and lightly grease cookie sheets with coconut oil.

In a large bowl combine flour, ground almonds, baking powder, lemon zest, and salt.

In a medium bowl mix the melted butter, maple syrup, and extracts. Add these wet ingredients to the dry ingredients and stir until well combined.

Form dough into small balls and place on cookie sheet. Press to flatten slightly. Then make an indent in each cookie with your thumb (or your child’s thumb).

Place ½ teaspoon of preserves in each imprint.

Bake for approximately 15 minutes or until edges turn a golden color.

Take out of the oven and allow to cool for a minute or two before removing cookies to a cooling rack.


With all of the wonderful real food bloggers around the web, I am finding more and more real food recipes. This saves a lot of guess work!

If you’re in a baking mood, you might enjoy trying some of the following cookies, breads and cakes made with whole wheat flour:

Do you bake with whole wheat flour? If so, do you have any tips for us? What”s your favorite thing to bake with whole wheat flour?

Reading Time:

4 minutes





  1. Elizabeth (Foodie, Formerly Fat)

    I think of regular wheat flour as being the grain equilavent of refined white sugar: nutritionally vacant. Whole wheat is a definite improvement.

    My son was recently diagnosed with a gluten intolerance. As a result I’ve been learning a ton about alternative flours. Most of them trounce even whole wheat flour in the nutrition department. We’d all do well to use a movement away from traditional wheat flour as a journey away from wheat altogether. It’s better even for those without gluten intolerance.

    • Kara E.

      Which alternative flours pack in more nutrition than whole wheat? I’d love to know, but have no clue on how to research that.

    • Stacy

      I think you are probably right, Elizabeth. I am very interested in trying out alternative grains and flours. I’d love to hear what your favorites are.

  2. Heidi @ Food Doodles

    I love this! I’m going to save this post to pass on – it’s so helpful to see all the different kinds of flours explained like that. I only very rarely use “white” flour anymore and it’s great. Once you get used to it, you’ll find it’s so much better. I do agree freshly ground tastes way better(and is better for you!) and if you’re planning on doing a lot of baking with whole wheat a mill is really worth it, it will pay for itself. Most often I make 100% whole wheat bread but I love making whole wheat cookies 😀

    • Stacy

      I agree about the grain mill. It is worth it! I love mine.

  3. Nisha

    This post is such a fabulous resource on whole wheat flour. I just recently started grinding soft white wheat and I’m hooked! Can’t wait to try this. I just stocked up on coconut oil, raw almonds, and raspberries. PERFECT timing 🙂

    • Stacy

      Awesome. I hope you like the cookies 🙂

  4. Kara E.

    I do love whole wheat for savory baking, but hadn’t thought to try it for sweets (probably because I try not to make them often). Next time I make cookies, these are going to be the ones. I hope they taste good.

    • Stacy

      I hope they taste good, too 🙂 We like them. Hopefully you will, too!

  5. Heather :) :) :)

    Oh, this looks really good. I am gluten intolerant, so I can’t have any wheat, rye or barley products. However, I’m going to find a way to make these gluten free 😉 🙂 Thanks for the recipe 🙂 Love and hugs from the ocean shores of California, Heather 🙂

    • Stacy

      If you find a way to make this gluten free, please share! I’m sure many others would love it, too.

  6. Laura Black

    Thank you for the substitution ideas and the cookie recipe. I started going back to basics and home cooking using organic ingredients a few years ago. I am always looking for new ways to incorporate healthier ingredients into my recipes. I love coconut oil and I also use coconut butter when making raw ice cream. It is so delicious and good for you. I will bake the cookies tonight. 🙂

    • Stacy

      I hope you like the cookies.

      Your ice cream sounds delicious!

  7. Sonja

    I LOVE using nuts, and grinding them to use as part of the flour! It adds extra protein, too, making the food more filling.

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