Recipe: Fruit, Nut, or Berry (or whatever you want them to be) Whole-Wheat Muffins

Whole-Wheat Muffins from 100 Days of Real FoodOh muffins, how do I love thee? Let me count the ways… First, you can serve these muffins as part of breakfast, lunch, or just by themselves as a snack. Second, they really are easy to make and with so many possibilities of what you can add to the muffin batter I am certain you will find a combination that you (and your kids) will love. Third, my kids scarf down their beloved customized versions, and I feel good about what they are eating. And last but not least, they freeze beautifully!!

I definitely have to give credit to my 5-year-old daughter for inspiring me to make these whole-wheat muffins. She got very excited one morning when I asked her what she wanted for breakfast and responded with “blueberry muffins!” We had not made muffins in years and I think she likes the idea of them because, well, the shape is strikingly similar to a cupcake! Once we got started my creative juices started flowing….these don’t just have to be blueberry muffins! I put strawberries in some and some leftover pear that I had on hand in others…and why not raisins? My 3-year-old loves raisins. So anyway, you get the idea how you can take the plain batter and add whatever flavors your heart desires. Make one big batch that’s all the same or each one different…and most importantly, have fun with it!

4.5 from 38 reviews
Fruit, Nut, or Berry (or whatever you want them to be) Whole-Wheat Muffins
Serves: Makes 12 Muffins
  • 1½ cups whole-wheat flour (I used King Arthur’s white whole-wheat flour)
  • ½ teaspoon salt
  • 2 teaspoons baking powder
  • ½ teaspoon cinnamon (We prefer fresh.)
  • ⅛ teaspoon nutmeg
  • 2 eggs
  • 2 tablespoons honey
  • 1 teaspoon pure vanilla extract
  • ¼ cup oil (I used coconut oil)
  • ¾ cup orange juice or apple juice
  • About 1 cup of total filling (berries, fruit, nuts, etc. – see below for details)
  • Muffin/Cupcake liners
  1. Heat oven to 400 degrees F.
  2. In a large bowl with a fork or whisk mix the flour, salt, baking powder, cinnamon and nutmeg.
  3. Make a well (hole) in the center of the flour mixture and pour in the eggs, honey, vanilla, oil and orange juice. Mix the dry and wet ingredients together – do not overmix.
  4. Now here is the fun part. If you are in a hurry just add 1 cup of blueberries, mashed up banana & nuts, or other filling of your choice. If you have 5 or 10 minutes extra (and some anxious helpers) do not add anything to the muffin batter before continuing with the next step.
  5. Line a muffin pan with liners and fill ⅔ to ¾ of the way full with batter. If you didn’t already add your filling, sprinkle 1 – 2 teaspoons of whatever you would like (from the list below or from your own creation) onto the top of each raw muffin in the pan. Then gently mix each one with a fork or spoon.
    Here are some options to consider for the fillings:
    - blueberries
    - diced strawberries
    - peeled and diced pears
    - applesauce
    - either diced or mashed up bananas and chopped walnuts
    - raisins and chopped pecans (I add an extra pinch of cinnamon to the muffins with this filling)
    - grated carrot and chopped walnuts
    - orange or lemon zest (only add ¼ to ½ teaspoon of zest per individual muffin)
    - a mix of dried fruit bits
    - jelly
  6. After the filling has been mixed into each muffin slide the tray into the warm oven and bake for 10 – 15 minutes or until a toothpick comes out clean. Serve warm or at room temperature and freeze some for a later date.
*This is a nut-free recipe if the optional nuts are not added. Nutmeg is not actually a nut.
We recommend organic ingredients when feasible.

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  1. Kara |


    I’m wondering if anyone had trouble with these sticking to the paper muffin baking cups? We made these tonight and they were great, but they all stuck to the paper.

    I’m going to grease the pan next time and not use liners.

    • Emily |

      I dont have muffin cups so I just greased my pan well and they popped out easily.

  2. Erin |

    Is there something I can sub for the juice? I never keep juice in the house anymore.

    • momof6 |

      Erin, I’m curious, too! I would think milk? But the juice also provides sweet flavor not just liquid, so you would need to up the sugar / honey.

    • Amy Taylor (comment moderator) |

      Hi Erin. You could use water and add a bit more honey. You could also use a combo of applesauce and water. I’ve not subbed with milk.

  3. Sunni |

    I just made these for my 2 year old who was recently diagnosed with an egg allergy and lactose intolerance. I made them with flax eggs and they turned out great. He just asked for another “mummin.” :)

  4. Marie Kropp |

    My coconut oil re-solidified when I added it to the dry ingredients. Is there a way to avoid that? Or does it not matter. (The muffins are still baking, so I don’t know what the final result will be.)

    • Amy Taylor (comment moderator) |

      Hi Marie. How did they turn out? Allowing colder ingredients to rest at room temp for a while can help as can mixing pretty quickly as you add the oil.

  5. Shannon B. |

    We have a coconut allergy, what can I substitute for the coconut oil?

    • Amy Taylor (comment moderator) |

      Hi there. Butter will work.

  6. GMASUZY |

    Love your recipes! We’d love them more in our diabetic household if they included nutritional information!

  7. Sarah |

    I WANT to like these muffins, but when I make them they come out dense and heavy. I don’t expect them to taste like boxed muffins- I understand they’re a whole different food- but I can’t help but think I could do something differently to make them more enjoyable. Can anyone help?

    • Amy Taylor (comment moderator) |

      Hi Sara. Have you tried using white whole wheat flour? It is 100% whole wheat but is lighter in color and texture.

  8. Jana |

    I just made these tonight as blueberry muffins. I added the zest of one lemon along with the juice of 1/2 lemon to add more flavor. I also sprinkled some organic sugar on top. Even after my modifications, I found these muffins to be pretty blah. I ate one warm with butter, but they were still missing sweetness. They came out light and I’m sure my 4 year old will love, but this one just didn’t do it for me. Most everything else that I’ve made from the cookbook I’ve been very pleased with. Maybe I’ll have better luck with the lemon raspberry?

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