Whole Grain Pumpkin Muffins

a couple of years ago

These whole grain muffins are fast, easy, delicious, and nutrient dense. Prep time does include an overnight soaking of the whole grains; however, evening-before prep and morning prep total just 10 minutes. Most of the magic happens while you are sleeping or getting ready in the morning. If you pop your whole muffins in the oven before your shower, you have a warm, moist, nutritious breakfast ready for you as you head out the door.

These muffins freeze well and stay moist in a covered container for several days. At least we think they do. They haven’t really stayed around long enough for us to establish that as fact.

Benefits of Soaking Whole Grains

Soaking whole grains prior to baking helps break down proteins and eliminates phytic acid, which prevents the body from absorbing nutrients such as calcium, magnesium, iron, and copper.

The very chemicals that are built into the seeds genomic structure to prevent them from germinating also prevent the body’s enzymes from properly digesting the grains. Soaking the seeds prior to baking, causes them to enter “germination mode.” They actually increase in vitamin content, and improved nutrition.

An added bonus is that the soaking also eliminates the gastric distress that often accompanies high-fiber foods. For extra nutritional value, try culturing your own buttermilk. The culture is available online and the process is both easy and economical. The bacteria used in buttermilk aids digestion and further eases the gastric discomfort associated with whole grains.

If you do not have buttermilk, you may substitute sour cream, plain yogurt, or soured milk in its place.

Cook Time

  • Prep Time: 10 minutes
  • Cook Time: 40 minutes
  • Yield: 6 large muffins or 12 small muffins


  • 1 2/3 cups Whole Grain Wheat Flour Mixture
  • 1 cup Pumpkin, Squash, or Sweet Potato
  • 3/4 cup Water
  • 2 Tbsp Buttermilk
  • 1/2 cup Coconut Oil
  • 1 cup Sugar
  • 2 Eggs
  • 1/2 tsp Baking Powder
  • 1 1/2 tsp Baking Soda
  • 3/4 tsp Salt
  • 1/2 tsp Cloves
  • 1 tsp Cinnamon
  • 1/2 tsp Nutmeg

Preparing Your Flour Mixture

For those with access to a grain grinder, we recommend using freshly ground wheat berries for nutrition and flavor. The ideal wheat berry for baked goods is spring wheat or white wheat. White wheat berries are available at most grocery stores, health food stores and even Wal-Mart carries them in their Super Centers.

If you would prefer to add low-gluten or gluten-free flours to the recipe, keep a ratio of 3 parts gluten to 1 part gluten-free flours. Some gluten is necessary to hold the muffins together. Good choices for gluten free grains are rice or corn meal.

Adding 2 tablespoons of ground flax seed to your flour mixture provides additional Omega 3 essential fatty acids.

If you do not have access to a grain grinder, don’t despair. You can grind your whole grain in a blender. Just incorporate a some of the liquid used in this recipe until you have formed a smooth paste.

Why Do You Need Wheat in This Recipe?

With all the wonderful flour options out there, why not forgo wheat completely? Unfortunately, these muffins were not designed for those on gluten-free diets. A certain amount of gluten is necessary to provide stability and structure. This is particularly true if a lot of add-ins, such as nuts or dried fruits are used. Gluten-free flours are just too fragile to keep the muffin together. Even though whole wheat flour is lower in gluten than all-purpose flour or bread flour, there is still enough gluten in the wheat flour to do the job.

whole grains

If you substitute lower-gluten flours for 1/4 of the wheat flour, you will have flatter, denser muffins that may not hold together as well as if you used the full amount of wheat flour. Weigh your nutritional needs against aesthetics as you decide which flours to use.

If you find that your add-ins add too much instability to the muffin and it falls apart, try incorporating 2 Tbsp all-purpose flour into your whole grain mixture. This will negate the effects of using low-gluten flour, but you will still have the nutritional benefits from using a wide variety of grains. Each whole grain provides its own unique nutrient profile.Displaying IMG_20160805_161742.jpg Displaying IMG_20160805_161742.jpgDisplaying IMG_20160805_161742.jpg

Gluten Content of Grains
Flour Gluten Flour Gluten
Almond free Quinoa free
Amaranth free Rice free
Barley low Rye low
Buckwheat free Sorghum free
Chickpea free Soy free
Corn free Spelt low
Millet free Tapioca free
Oat free Teff free
Pumpernickel low Whole Wheat low


  • Prepare you wheat flour mixture. You can use pre-milled flours or grind your own. Select the grains you wish to combine. White wheat berries produce lighter muffins than red wheat does.  Any mixture of flours is acceptable as long as you keep to the ratio of no less than 3 parts low to high gluten flour to 1 part gluten-free flour.
  • Place your flour, pumpkin, water, buttermilk, and coconut oil in a mixing bowl. Mix all the ingredients thoroughly. Cover and set on the counter overnight. Batter should be easily stirred with a spoon but not soupy.
  • The next morning, incorporate the rest of your ingredients and mix well to distribute the spices and salt evenly. If you wish, you can place the batter into the refrigerator for use later in the day. Make sure to bring the batter to room temperature before proceeding with the next steps.
  • Pour the batter into greased muffin tins and sprinkle the tops lightly with sugar. Large crystals, such as you would find in Raw Sugar make a pretty and flavorful topping. Do not use too much. Too much sugar makes the tops heavy and the muffins will sink during baking.
  • Bake at 325 degrees until an inserted toothpick comes out holding crumbs instead of wet batter. The muffins will seem more “moist” than what you might expect. Bake approximately 40-45 minutes.
  • Allow to rest in the pan 10 minutes and then turn onto a cooling rack. You may need to loosen the tops from the pan with a plastic knife if the sugar has crystallized around the top.

How Many Calories?

These muffins make a low-calorie meal when eaten by themselves and provide enough fiber and protein to leave you feeling satisfied. Each muffin as approximately 217 calories, in a ratio of 3:1, carbohydrates to good fats.

Low-fat alternatives can be created using applesauce in place of some or all of the oil. Reductions in the amount of sugar using one of the provided sugar substitutes can lower the amount of carbohydrates in each muffin.

We are of the opinion that they should be enjoyed in their fullness, as a complete meal, and you can feel secure in knowing that the fiber will bind the fat and help regulate your blood sugar.

Additional Comments

Always make sure to adjust your moisture content based upon any substitutions. The batter should be a thick paste, spoon-able, but not mold-able like cookie dough.

In addition you can add ingredients such as chocolate chips, nuts, coconut, or dried cranberries. One of our favorite variations is to add 2 tsp orange peel, 1/4 cup dried cranberries and 1/4 cup chopped pecans.

Olive oil or butter can be used in place of or in combination with the coconut oil. Replacing all the coconut oil with either olive oil or butter results in a more dense muffin. A mixture of coconut oil and butter is our preference.

A delicious way to serve these muffins is with cream cheese spread or a small dab or jam.

We would love to hear how you have tweaked this recipe successfully. Leave a comment sharing your favorite ingredient combinations.


 1 Cup of Buttermilk Equals 1 Cup of Sugar Equals Instead of Pumpkin
1 Tbsp Vinegar + 1 C Milk 3/4 C + 1 Tbsp Honey Mashed Bananas
1 Tbsp Lemon Juice + 1 C Milk 3/4 C Maple Syrup Butternut Squash
1 3/4 tsp Cream of Tartar + 1 C Milk 1 1/3 C Molasses Applesauce
1 C Plain Yogurt 3/4 C Juice Concentrate Grated Zucchini
1 C Sour Cream n/a Grated Carrots

Sugar and pumpkin substitutes may affect the amount of water needed for the recipe. Do not replace more than half the sugar with molasses and add 1/4 tsp of baking soda when using it.


Saco Cultured Powdered Buttermilk Blend, 12-ounce Can  ARROWHEAD MILLS FLAX SEED,OG2,S1258664, 1# Viva Labs The Finest Organic Extra Virgin Coconut Oil, 16 Ounce Sugar In The Raw/Unrefined, 32 Ounce Box
Kim Schmutzler

About the Author

Kim Schmutzler

Kim and her husband, Craig, live in Overland Park KS where she successfully manages a marketing company and homeschools her two children still at home. Twenty-two years of juggling business and homeschooling has taught her a thing or two about time management. In addition to work and family, Kim helps her husband with the College and Career class at the church and also directs the Children's Music Ministry and drama team. The Submissive Spirit was born from her desire to reach out to other Christian women across the globe and share encouragement and the love of Christ.

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