Whole Wheat Blueberry Muffin Recipe

by Jimmie

How to cook homemade blueberry muffins from scratch using whole wheat flour and honey. These muffins are clean eating and full of nutrients.

Clean Eating Whole Wheat Blueberry Muffins

Made From Scratch With Real Foods

Forget store bought muffins. It is not difficult to make homemade muffins, and the results are so worth the small effort. Blueberries are nutritional powerhouses. So add more to your diet with these decidedly healthy muffins.

Whole Wheat Blueberry Muffins
Whole Wheat Blueberry Muffins

Whole Wheat Blueberry Muffins Ingredients

Recipe Makes One Dozen Regular Sized Muffins

Dry Ingredients

  • 1 cup whole wheat flour
  • 1/2 cup oats, blended in food processor or blender until fine
  • 1/4 cup white flour
  • 2 tablespoons ground flax seed (optional, but adds nutrition)
  • 1 teaspoon salt
  • 2 teaspoons baking powder

Wet Ingredients

  • 1/4 cup unsweetened applesauce
  • 3 tablespoons melted butter, plus additional butter for greasing the pan [or omit the applesauce and double the butter to 2/3 cup]
  • 1 egg
  • 1/2 cup honey [OPTIONAL additional 1/2 cup sugar]
  • zest from one lemon (approx. 1-2 teaspoons)
  • 1/2 cup milk (any kind will do)

 The Berries

  • 1 1/2 cups fresh or frozen blueberries

Photos Step by Step

Wet Ingredients
Wet Ingredients
Add Dry Ingredients
Add Dry Ingredients
Muffin Batter
Muffin Batter
Batter in Muffin Tins
Batter in Muffin Tins

Whole Wheat Blueberry Muffins Directions

Preheat oven to 375°.

Grease 12 non-stick muffin tins with melted butter, using a silicone pastry brush. (You can see my Wilton pan and Le Creuset pastry brush below. Love them.)

Mix dry ingredients. Toss a few spoonfulls of it into the blueberries and toss gently to coat.

In a large mixing bowl, combine wet ingredients except milk. Whisk well and then add milk. Whisk again and then put away the whisk. You are finished with it.

Add dry ingredients and fold a few strokes with a wooden spoon. Stop before it is fully mixed. Add blueberries and gently mix. Stop as soon as the flour is mixed in. Do not over mix, and by all means do not beat. (Muffins get tough when overworked.) This batter is thick.

Spoon batter into the greased muffins tins, using a 1/3 cup measure. That's about how much batter to put into each tin, and it makes scooping it easier.

Bake in center of oven for 12-15 minutes.

These muffins, because of the whole wheat flour and honey will be much darker than a white sugar and white flour muffin. 

When the muffins test done, allow the pans to cool for 3 minutes. Then remove the muffins from the pans to cool completely on wire racks.

These are great slathered with butter.

Makes 12 regular sized muffins.

Note about sweetness

These are not a very sweet muffin. For me, they are perfect. I don't like super-sweet baked goods. The tartness of the berries plus the lemon rind makes these only slightly sweet. If you have a sweet tooth, add the additional white sugar.

Favorite Tools from My Own Kitchen

That I Used to Make These Blueberry Muffins
Le Creuset Silicone Pastry Brush, Cherry
Le Creuset
Only $12.00
Wilton Avanti Everglide Metal-Safe No...
Only $13.99
WMF Profi Plus Stainless-Steel Lemon ...
Only $8.00

Get the Butter

The Muffins are Ready
Muffins Ready to Eat
Muffins Ready to Eat

Sweetening Your Muffins

What Do You Use?
  Display results
Thanks for voting!

Blueberries -- Fresh or Frozen?

Which are better for muffins?

Frozen are better.
Digby_Adams on 06/19/2011

I use frozen because I prefer wild blueberries and I can't find fresh wild blueberries.

RhondaAlbom on 06/02/2011

Frozen for muffins or pancakes but fresh for everything else.

Fresh is always best.
Dianne on 06/03/2011

I have blueberry bushes in my back yard, so always fresh!

Guest on 06/02/2011

Fresh all the way!

nightbear on 06/02/2011

I love fresh ingredients and I like a variety of fresh fruits.

eclecticeducation on 06/02/2011

I like fresh the best.

kab on 06/02/2011

Fresh! Frozen = mushy.

Jimmie on 06/02/2011

I prefer the texture of fresh, but I've been known to use frozen.

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The zing of lemons balances the dense texture of a traditional pound cake. In this recipe, you juice and zest fresh lemons for the maximum lemon flavor.
Updated: 12/30/2011, Jimmie
Thank you! Would you like to post a comment now?


cazort on 04/05/2013

Oh my gosh, this sounds like a recipe I would absolutely love...no sugar, only unsweetened applesauce as the source of sweetness. I love this! This is exactly how I like to bake. Most mainstream recipes are way too sweet for me...I love baked goods that have only a mild sweetness. And I love how muffins and other sweets come out when using whole wheat flour...they are so much richer and more robust.

Digby_Adams on 06/19/2011

My husband and I have a mixed marriage - I have a sweet tooth and he doesn't. But I think these blueberry muffins will make us both happy. I've given you a big thumbs up!

puzzlemaker on 06/12/2011

These look amazing. I'll love to have a few here in front of me smothered with butter.

Mike on 06/12/2011

They sound almost as good as a puppy burger and fries!

Dianne on 06/03/2011

For years I've been making blueberry pie and leaving out the lemon zest that it called for. One day I was making a pie and happened to have some lemons so I added the zest. I couldn't believe the difference it made! Really brightened up the flavor. I always add it now.

lakeerieartists on 06/02/2011

This is a great blueberry muffin recipe. My daughter has become very strict in her eating habits, and will only eat whole wheat muffins. I will have to make these for her. I will probably not include the lemon though. Let you know how she likes it.

mbgphoto on 06/02/2011

Blueberries make everything taste better...well almost :)

Guest on 06/02/2011

I like blueberry "anything". This does sound really yummy. Will have to try this one.

nightbear on 06/02/2011

Very fun! Did this come from the natural cooking cookbook that you needed over in China?

RhondaAlbom on 06/02/2011

Yummy! I love blueberry muffins and your pictures make this page so attractive that I have to try these muffins!

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