Whole Wheat Peanut Butter Blossoms with Fresh Milled Flour

Name: Whole Wheat Peanut Butter Blossom Cookies with Fresh Milled Flour
Prep time: 10 min
Cook time: 7 min
Total time: 137 min
Ingredients: 1/2 cup butter (1 stick); 1/2 cup peanut butter (125 grams); 1/2 cup dark brown sugar (110 grams); 1/2 cup white sugar (110 grams); 1 egg; 2 tablespoons milk; 1 teaspoon vanilla extract; 125 grams hard white wheat berries, milled into flour (about 1 cup flour); 125 grams soft white wheat berries, milled into flour; 1 teaspoon baking soda; 1/2 teaspoon salt; additional white sugar for rolling dough balls; 30+ chocolate kisses

These whole wheat healthy Peanut Butter Blossoms are the PERFECT cookie for your Christmas cookie platters this year! Remade using fresh-milled flour and nutrient-dense ingredients, it still tastes exactly like the regular version you know and love!

For more cookie variety, you’ll love my healthy molasses oatmeal cookies and dark chocolate macadamia nut cookies.

A cooling rack of fresh milled peanut butter blossoms.

Recipe at a Glance: Healthy Peanut Butter Blossoms

Prep Time ⏱️	Fridge Time ❄️	Bake Time 🔥	Total Time ⏰
10 mins	2 hrs	7-8 min	2 hrs 17 mins

🍽️ Servings: 30 cookies
👍 Difficulty: Easy
😋 Recipe Highlights: Wholesome ingredients, soft interiors, crackly tops–just like the classic cookie recipe but made with whole grains!
🛒 Featured Ingredients: Hard white wheat berries, soft white wheat berries (or bagged whole wheat pastry flour), butter, peanut butter

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Nothing says Christmas Magic like a pan of warm peanut butter blossoms right out of the oven - the soft, crackly tops, warm peanut buttery scent, and that little chocolate kiss melting right in the center.

What if you could enjoy that classic holiday favorite with the wholesome goodness of fresh-milled whole grains, without losing any of the flavor or texture?

There was no way I could let a Christmas season go by without making my classic Peanut Butter Blossoms. I knew I had to find a way to make them perfect with fresh milled whole wheat flour!

If you want a fresh milled Christmas cookie that is a touch better-for-you, these healthy peanut butter blossoms are going to become a holiday favorite in your kitchen. For more fresh milled flour recipes, try my whole wheat sandwich bread and whole wheat sourdough bagel recipe.

Why You’ll Love This Recipe

Perfectly golden, soft, and irresistibly peanut buttery-these whole wheat peanut butter cookies have the perfect texture and flavor that vanish off the tray almost as fast as you bake them!

Jump to:

Recipe at a Glance: Healthy Peanut Butter Blossoms
Why You’ll Love This Recipe
Whole Wheat Peanut Butter Blossom Ingredients
How to Make Whole Wheat Peanut Butter Blossoms
Fresh Milled Flour Cookie Tips & Tricks
Other Fresh Milled Flour Recipes
Whole Wheat Peanut Butter Cookies FAQs
Other Christmas Treats
📖 Recipe
💬 Reviews

Whole Wheat Peanut Butter Blossom Ingredients

The ingredients needed for healthy peanut butter blossoms on a dark background.

I make these healthy peanut butter blossom cookies more nutrient-dense by carefully choosing my ingredients. For a complete list of ingredients, see the recipe card.

Fresh-milled, whole wheat flour – I use a blend of hard white wheat and soft white wheat. If you prefer to use only one type of wheat berry, I recommend soft white wheat and add an additional 15-20 grams to the total quantity.

There is less protein in soft wheat, which is what keeps it light and fluffy, but by using a bit of hard white wheat in the recipe, this helps keep the cookies from spreading too much.

Bagged whole wheat flour works, too. Whole Wheat Pastry Flour is a great option.

Butter – Instead of vegetable shortening, we use real butter. For an added punch of nutrients, choose grassfed butter! I have used both salted and unsalted butter, and it will work either way. Choose whatever you prefer to bake with.

Note: A stick of butter uses about 1/4 teaspoon of salt on average. With an amount that small, I did not notice much of a difference in salty flavor either way across the whole batch of 30 cookies, so no need to alter the salt quantity. Simply just use the butter you want to use.

Dark brown sugar – Dark brown sugar has a higher amount of molasses, which keeps the sugar softer and translates to cookies with a little more moisture, keeping them from getting too hard.

Hershey Kisses – I love using dark chocolate kisses when I can find some! Dark chocolate is a great option for more heart-healthy fats, antioxidants, and minerals.

Peanut Butter – I like to use thicker natural peanut butter (such as Good & Gather (Target’s store brand) or Skippy Natural). While these are not the “purest” peanut butter, they have simplified ingredients and the perfect texture for baking.

I have used natural, runny peanut butter in the past and it will work if its all you have. If that’s the route you go, I recommend adding an extra 30 grams of flour.

How to Make Whole Wheat Peanut Butter Blossoms

Here is how you make whole wheat peanut butter Christmas cookies!

A mixing bowl of wet ingredients for cookies.

1. Mix Wet Ingredients.
Cream together the butter, peanut butter, dark brown sugar, and white sugar in a stand mixer for about 2 minutes or until nice and smooth. Add the egg, milk, and vanilla and mix until combined.

A white bowl of the dry ingredients for the fresh milled cookies.

2. Mix in Dry Ingredients.
Mill your flour (or measure 1 3/4 cup bagged flour) into a bowl. Add the baking soda and salt. Whisk to combine, then pour the dry ingredients into the mixer bowl of wet ingredients. Stir until evenly mixed.

A white bowl of finished dough ready for the fridge.

3. Refrigerate Dough.
Put the cookie dough into a bowl, cover, and refrigerate for two hours (if using bagged flour, refrigeration is not necessary).

This allows the fresh flour to fully absorb the liquids in the dough. DO NOT SKIP THIS or your cookies will be flat soup. :/

If you’re in a hurry, you can add 30-60 more grams of flour to help the cookies keep their shape, but I recommend following the intended instructions for best results.

4. Scoop & Sugar Coat Cookies
After refrigerating, preheat the oven to 375°F. Fill a small bowl with extra white sugar for rolling the cookie dough balls.

Take the cookie dough out of the fridge. Using a standard-sized cookie scoop, scoop out a cookie ball, place in a small bowl of sugar, and roll until coated.

Place each ball onto a parchment-lined cookie sheet. Do not flatten the dough balls with your hand–they will spread too much in the oven if you do.

Evenly space your dough balls with at least 1.5-2 inches of space between them on the cookie sheet–do not crowd them.

5. Bake Cookies.
Bake these cookies at 375°F for 7-8 minutes until the tops crackle and they are light golden brown in spots. Your oven temp/time may vary, so watch them carefully.

While baking, prep your chocolate kisses by removing the wrappers and set aside.

Putting Hershey kisses in the middle of the baked cookies.

6. Place Chocolate Kisses and Cool.
When the cookies are done, remove the cookie sheets from the oven. Immediately place a chocolate kiss/star in the center of each one. Allow cookies to cool on the cookie sheet to fully set before removing them.

A plate of whole wheat peanut butter blossoms Christmas cookies.

Do Not Skip the Refrigeration. Freshly milled flour cookie dough needs ample time to absorb liquids.

You will notice when you first mix batters and doughs with fresh milled flour, they may seem mushy. This is because not all of the liquids are absorbed yet, and the flour is not fully hydrated.
You can’t rush this process–the dough just needs time. Some people add extra flour to combat this rather than do a dough rest, but I avoid adding extra flour if possible because you risk your final product being drier or more crumbly.

Cookies may bake faster than you’re used to. Watch them carefully. When I make this recipe with white bagged flour, I usually bake for 9-10 minutes. With fresh milled flour, I do 7-8. However, all ovens are different! Keep an eye on them and adjust for your oven.

If your dough is still too mushy after refrigeration, add a little more flour before scooping–start with 15 grams of flour at a time and stir it in. Once the dough holds a round shape well, start scooping!

Other Fresh Milled Flour Recipes

If you don’t want your baking adventures to end, some of my favorite fresh-milled flour recipes are my Cheesy Garlic Pesto Knots, my Sourdough Sandwich Loaf with Whey, my 100% Whole Wheat Sourdough Batard, and my Pumpkin Spice Sourdough English Muffins.

Visit my fresh milled flour baking category to explore more of our family favorite, tried & true recipes.

Whole Wheat Peanut Butter Cookies FAQs

Can I use whole wheat flour in peanut butter cookies?

Yes, you can use whole wheat flour in peanut butter cookies! However, you must be mindful of the protein content in the flour for best results. The best type of whole wheat flour to use for cookies is generally a soft white wheat or an ancient grain with a lower amount of gluten–this keeps cookies soft. However, there are other slight adjustments you can make to the recipe techniques to improve results, too, such as refrigerating the dough and watching the bake time carefully.

What happens when you use whole wheat flour instead of all purpose flour?

When you use whole wheat flour, especially freshly milled wheat flour, instead of all purpose flour without any other adjustments, you will alter your final results. How much will depend on the particular recipe, but with a store bought bag of whole wheat flour, your cookies will usually be more dense and heavy. With freshly milled flour, your cookies will spread completely flat.

That said, you can significantly improve your whole wheat baking results by implementing certain techniques, such as weighing your flour, using the correct type of wheat, refrigerating the cookie dough before baking, and more.

Are whole wheat cookies healthier?

Whole wheat cookies offer more health benefits over cookies made with refined white flour, such as higher amounts of fiber, B vitamins, folate, iron, and antioxidants. If you’re looking to add some nutritional components to your cookie recipes, whole wheat flour is a great choice with the right techniques enacted to ensure the best results.

However, a cookie is still a dessert and should be consumed in moderation as part of a balanced and varied diet.