Blueberry, Fruit, Nut, (or Anything You Want) Whole Wheat Muffins

61 Reviews / 4.3 Average
I love a good muffin recipe that you can really make your own by switching up the ingredients. These whole-wheat muffins taste delicious with fruit, nuts, or berries in them. Make sure to make a double batch to freeze or later.
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Blueberry fruit filled whole wheat muffins

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Oh muffins, how do I love thee? Let me count the ways… First, you can serve these blueberry (or anything you want) whole wheat 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 that 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!!

The inspiration for these blueberry, fruit, nut, or anything you want whole wheat muffins

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 make each one different…and most importantly, have fun with it!

Are whole wheat blueberry, fruit, nut, etc. muffins healthy?

The whole wheat muffin batter that I used in this recipe is made from real food ingredients. That means no processed flour or refined sugar! And the overall amount of sweetener used is reduced compared to store-bought muffins. When you add healthy ingredients like fruit, veggies, and nuts, whole wheat muffins end up being a pretty balanced breakfast or snack.

If you’re new to doing real food swaps in your house, this is a great replacement for busy families to skip processed cereal in the mornings. Plus you can sneak an extra serving of fruit or veggies in for picky eaters!

Tips before you get started making these blueberry (or anything you want them to be) whole wheat muffins:

Why does this recipe use juice?

I’ve used both apple and orange juice to make this muffin recipe, it just depends on what I have on hand. The juice adds liquid/moisture to the recipe, which is needed for these whole wheat muffins to bake properly. It also doubles as a substitute for refined sugar.

Some people may find orange juice too bitter, so in that case I’d recommend just using apple juice (we prefer unfiltered organic juice not from concentrate). You could also substitute another juice variety of your choice such as pear. Just make sure it’s 100% juice!

Finally, you can also substitute the juice with milk if you prefer. The muffins will still turn out moist, but you may find them less sweet. If you opt for milk, I suggest using sweeter mix ins or adding a bit of additional honey, depending on your preference.

Can you use frozen blueberries or raspberries in whole wheat muffins?

Frozen blueberries and raspberries should bake the same as fresh berries in this recipe. Just make sure your berries don’t melt while you’re mixing them in! If the frozen berries start to melt, they’ll start to release juice into the batter and may not hold their shape as well.

What foods make good fillings for muffins?

I call these “whatever you want them to be” muffins because you can add pretty much anything to the batter, and they still turn out. You can also combine more than one filling for unique flavors!

Fruit (fresh, frozen, or dried, for sweet muffins)

  • Blueberries
  • Raspberries
  • Diced strawberries
  • Chopped and peeled apple or pear
  • Applesauce
  • Mashed banana
  • Raisins
  • Dates
  • Dried cranberries
  • Lemon or orange zest

Vegetables (for savory muffins)

  • Grated carrots
  • Zucchini
  • Pumpkin
  • Corn
  • Sweet potato
  • Bell pepper
  • Garlic
  • Onion

Nuts (chopped)

  • Pecans
  • Almonds
  • Walnuts
  • Pistachio

Dairy & Meat

  • Grated cheddar cheese
  • Cream cheese
  • Sour cream
  • Cubed pieces of cooked meat (great for a breakfast muffin!)

If your whole wheat muffins with dried fruit, nuts, or other mix-ins come out dry

Sometimes homemade muffins can come out dry. This usually happens when you scoop the flour on the heavier side or slightly under measure the liquid in the recipe. It can also happen if you’re using dried fruit or nuts that absorb the liquid (vs fresh or frozen ingredients that have a lot of internal moisture).

Depending on how dry they are, you can add ¼ to ½ cup of applesauce, Greek yogurt, mashed banana, or grated zucchini.  

How to keep muffins from sticking to the pan

I always bake my muffins inside muffin liners to make it easier to remove them. If you’re using paper liners, look for the parchment variety. Another idea is to use foil cupcake liners and lightly spritz them with an oil of your choice.

If you don’t want to use liners, you’ll need to properly grease the muffin pan. Use your favorite method, or try spreading butter inside the muffin tray’s cups, then dusting with whole wheat flour. Shake off the excess.

Other muffin recipes you might like

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Recipe Rating

  1. 4 stars
    I just made these using the recipe as written adding blueberries. They turned out good but for anyone expecting a sweet muffin this isn’t it.
    I recommend using
    If You Care
    unbleached paper baking cups. Nothing ever sticks to them!

  2. 5 stars
    I omitted the eggs, increased the apple juice to a cup, added frozen blueberries and baked in an 8×8 glass pan for about 40 minutes. The result was a very soft and delicious coffee cake. Love it! Will definitely make again!

  3. Excited to try these but not sure when you all reformatted your website but I can no longer save your *amazing* recipes in my family’s Cozi app like I used to. . SUPER sad face about this!

  4. Michelle Merritt

    I was craving some muffins, which I haven’t had for a while, but I didn’t have any orange juice or apple juice. I did, however, have apple butter on hand. I mixed half apple butter and half water in place of the juice. Not dry at all! I also added chopped walnuts and cranberries. Love this recipe!

    1. Amy Taylor (comment moderator)

      Hi there. Sorry, but we do not provide nutrition breakdowns of our recipes. We just want people focusing on getting more real food into their lives by dropping the processed stuff. : )

  5. I’ve made these several times and they’ve been wonderful every time. This time, I made blueberry muffins and used flax eggs because I was out of regular eggs. They didn’t turn out as good. Kinda dry. I would suggest using regular eggs and not an egg substitute for these.

  6. I just made these muffins and the oil came out quite a bit during baking and left oily muffin liners and oil in the pan. I think it is because I used cold apple juice and frozen blueberries – the coconut oil didn’t have a chance to melt into the batter. Do you melt the oil before baking with it?

  7. 5 stars
    Just made these today. They are fluffy light and I’m having trouble not eating all of them! I replaced 1/5 cup of the wheat flour for white so that they are less chewy, added 1/8 tesp of ginger and subbed applesauce for the oil. Strawberries were my mix in.

    I plan on making a second batch this week because I already know the ones I made won’t last.

  8. I made these today and they were not sweet enough for my kids so I added a few tablespoons of maple syrup to the second batch and they were perfect for us. Everyone has their own desired level of sweetness! :) They did stick to the liners a bit but we didn’t mind. I’ll be using this recipe again! Thank you!

  9. Amanda Bruckhart

    Hi! I just recently made these muffins and found them to be dry. Do you have any suggestions on what I can do/add to make them not so dry? Thanks!

    1. Amy Taylor (comment moderator)

      Hi there. Could you have gone a little heavy on the flour. My answer to dryness is applesauce or yogurt added to the recipe. :)

      1. How much applesauce or yogurt would I use? Also is that instead of another ingredient or in addition to? Thank You

  10. Hi, just found your site and I made these muffins tonight and they are a hit! I have 1 big problem though- they are sticking to the paper wrappers terribly! What can I do to avoid this? Are the liners/wrappers necessary? Thank you!!

    (I followed your base recipe exactly, and added 1 cup of frozen blueberries)

    1. Amy Taylor (comment moderator)

      Hi. I’ve baked them in a muffin pan without paper. I buttered/coconut oil-ed the pan first. Cleaning the pan was far more difficult without the paper. :) I have spritzed my papers with oil, too. It helps.

  11. Making these now! I didn’t have any juice, so I added apple sauce and then sate a tablespoon at a time until I had what I thought was a good muffin batter consistency. Crossing my fingers they turn out!

    1. 5 stars
      They turned out really great! In the previous comment I meant that I added water until the desired consistency. I also peanut butter/oat/almond struesel from a different site. I slightly overbaked tgem by 1 or 2 minutes, but they were still good. I can’t figure out how to upload a picture, but I would if I could!

  12. 2 stars
    I made these muffins very recently with frozen blueberries. I was not impressed with the results nor was my family. The muffins had a slightly bitter flavor. And they weren’t sweet enough. My spouse described them as “healthy tasting” which was not meant as a compliment. I wouldn’t make them again. I question why the orange juice in the recipe and would suggest readers try a different recipe for muffins.

  13. Thank you for This recipe! I tried this last night with fresh blueberries. They were fantastic warm out of the oven with a little butter spread on top. I was honestly worried that my kids would find them a little bland as these are not sweet, but they loved them and asked for them in their lunch again for tomorrow. Has anyone tried this with chocolate chips? I might try it.

  14. I like to serve freshly baked muffins. To speed things up in the morning, the night before I mix the dry ingredients in a bowl, leave it covered on a counter and mix the wet ingredients in a large measuring cup. and store it in the refrigerator, In the morning all I have to do is mix the two and scoop the batter =
    into muffin pans and bake them ……. usually takes about 30 minutes.

  15. Any substitutes for the orange/apple juice? I don’t really want to add more sugar if I’m trying to make a healthy alternative to typical muffins. Can it be left out?

      1. Plug ingredients individually into and it will give you total. Depending on what you put in it , it would be different from the recipe anyway. Good on you for taking control of your Diabetes!

  16. Hello! I’m planning on making these and the banana pancakes and freezing them to take on an upcoming vacation. My question is… it best to pull them out of the freezer the morning of and zap in the microwave? Or should I thaw them out in the fridge the night before and then microwave them the next morning? Thanks so much! This website has been so helpful to me and my family!

  17. Hi, this seems like a great base recipe for customising & baking your own muffins. What does the juice in the recipe do? Is it just for moistness? If so , can I add mango juice or milk or anyother ?

    1. Amy Taylor (comment moderator)

      Hi. The juice provides moisture and sweetness so mango juice should work just fine.