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

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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565 thoughts on “Blueberry, Fruit, Nut, (or Anything You Want) Whole Wheat Muffins”

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Recipe Rating




  1. These were delicious. I used half wheat and half spelt (it is lighter like it was stated on the pumpkin spelt muffin recipe). Try using the power C-machine Naked brand juice instead of apple or orange! Wow it was a great choice. It has orange and apple in it, but also strawberry, mango and peach and guavas….nice and sweet but natural!

  2. I just made these and I’m completely new to coconut oil (I know, for shame, shaaaaaaame!) … but am I supposed to melt the coconut oil before I put it in the batter?

  3. 4 stars
    I just baked these today, and although they are tasty they lack in color. What do you recommend for giving my muffin a nice golden brown color?
    Thanks in advance.
    Xoxo

  4. TERRY CHRONISTER

    4 stars
    I have used this recipe twice – once with srawberries and pecans, and once with overripe bananas and walnuts. The first batch wasnt my favorite out of the oven, still had a bit of that bitter wheat flavor, but the next day I microwaved them, and the flavor was improved. I mashed the overripe bananas so they blended with the dough, and this batch was delish, did not taste like a wheat muffin. Only chage I would make is I used 1 cup (2 bananas) of bananas and 1/2, maybe of walnuts, the dough needs to be saturated with walnuts for texture. Good base recipe to play with to your liking.

  5. 4 stars
    I made these and my daughter loved them (she hates whole wheat) The next batch I substituted 1/2 cup ground flax seed for the whole wheat flour, added 2 cups of blueberries and 1/2 cup of walnuts and I used red palm oil.
    Tasted great.

  6. 5 stars
    I just made these this morning and they were so good! I was making them for toddlers so I did half banana and half blueberry. I wanted the banana to add sweetness. The little girls LOVED them. My daughter is used to food like this, but the girl I nanny is finicky with food, but she was shoving these in her mouth. And I loved them too. I used apple juice because orange juice can be bitter and some comments were about it tasting bitter.
    Thanks for always posting high quality recipes! I appreciate your integrity as a blogger!

  7. I made these last night with my almost 3 year old. The muffins were quick and easy and very tasty! My mother in law would like them sweeter, but those that only eat whole grain – they are a treat to feel great about! We added raisins, apricots and bananas.

  8. These muffins are great – so easy to prepare, not too sweet and my family loves them. I used home made apple sauce instead of juice (probably changes texture a little), hand picked (frozen) blueberries twice and apple/date pieces the third time. I’ve been using paper cups, but for my first baking I did not have any so cut small circles from parchment and placed in bottoms of the pan, and greased sides. Every time the muffins have come out clean and the papers peal off easily. The hardest part of this recipe for me is grinding my whole wheat flour from wheat berries before combining ingredients, and I used an organic, aluminum -free baking powder: There was no bitterness at all. These are definitely the most hassle free – tastiest muffins I’ve ever made! This is the first review I’ve ever written, so it must be a good recipe for me to take the time to write about it.

  9. 5 stars
    Excellent. I used apple cider. Mixed frozen blueberries right into the batter. Just the right amount of spice and sweetness. Was surprised that they really did bake to perfection in just 15 minutes. Thank you!

  10. I made these today with my little girls and we all loved them. We actually used milk instead of juice and just used diced bananas. The muffins turned out great. Not sweet except for the bananas, but for us the sweetness was perfect. It really lets the fruit shine through. Awesome recipe! Thanks!

      1. It did for us. The juice would probably make them sweeter, but I liked them with milk. I made them a second time and added diced thawed peaches. Also delicious! I also subbed applesauce for the oil, and that worked well too.

      2. Did everyone cook the muffins at 400 degrees? That seems a little hot? Just curious, as I’m accustomed to baking muffins closer to 350.

  11. Extremely bitter… Too much baking powder? We made them exactly as written with frozen blueberries. We’ve had bad luck with Clabber Girl baking powder, but this recipe also seems to call for much more than Lisa’s other muffin recipes — 2 tsp vs 1/4 tsp plus baking soda, etc.

    1. Did you use orange juice? I feel like orange juice can be very bitter. I made these with apple juice and they weren’t bitter at all.

  12. 4 stars
    I made these twice, once with mulberries and once with mixed berries. Both times I used apple juice. The texture was good, but they weren’t very sweet. We don’t eat a lot of sweet things in our house, so they worked our okay for us. Next time I may try cider to see if I can get them just a tad sweeter.

  13. 5 stars
    Love these! Close to the old BH&G Cookbook muffin recipe that I grew up with — my recipe called for milk but I subbed OJ on a regular basis. I loved my old recipe because they were NOT sweet, and you could taste the fruit, so I love this one just as much, and the whole wheat makes them “nuttier.” Allow the muffins to cool completely & most muffin papers will slip right off, BUT I picked up a “professional” brand at a scratch-n-dent grocery and those suckers will NOT come off — not the fault of the muffins! These are GREAT with blueberries that were u-picked and frozen, and a few drops of lemon extract in place of the vanilla. Yummmmm!

  14. 1 star
    Not a fan, I read these reviews after I mixed everything up, right before baking so I added more honey and maple syrup. I still didn’t like the outcome.

  15. 4 stars
    I made these with blueberries this morning. Both my daughter and I liked them. I used apple cider because I think it sweetens things better than orange juice. We don’t eat much sugar so thought they were sweet enough. I could actually taste the honey flavor since there wasn’t a bunch of sugar to cover it up. We’ll be making these again.

  16. 2 stars
    I made these today with strawberries and banana as the “add in”. I don’t like really sweet muffins, but these weren’t sweet at all. They also stuck really badly to the liners. Guess it’s back to the drawing board, I won’t try this recipe again. Too bad I made a double batch to use up some berries that were getting a bit old.

  17. 4 stars
    I made these for the first time today for my muffin-loving kiddos, and I added frozen blueberries. I have grown used to the less-sweet real food baking recipes, but this one came out very slightly sweet, almost not sweet at all. Otherwise, it was a good muffin! I added everything exactly except I added equal parts unsweetened applesauce and olive oil instead of just oil. Should I add a bit more honey next time or some maple syrup? I liked them but I think the kids would like them more if they were a bit sweeter. Just not sure how to slightly sweeten them vs over-sweeten them. LOVE this site, and your pumpkin muffins are our favorite around here! :)

  18. I just popped these in the oven. I used olive oil. I grabbed a handful of mixed frozen fruit (strawberry, blueberry, cherry, raspberry) and stuck them in my ninja. I made very small peices of fruit and mixed them in after separating the plain batter into cupcake liners. Then made some with thinly sliced banana and a dollop of cbs nuts peanut butter (1 ingredient pb). I’m pretty excited, I’ve always had good luck with Lisa’s recipes. My son loves muffins in his lunch!

  19. 5 stars
    I made these the other night with strawberries. My daughter’s devoured the left overs for breakfast the next day and requested them for school lunches. My biggest issue is how do I freeze these? I generally just put things in zip lock bags, is that enough or should I do something more? They love grabbing food from the freezer and packing their own lunches.

    This website has inspired them with so many ideas for their lunches. Thank you.

    1. Amy Taylor (comment moderator)

      Hi. Ziplocs will work fine. I get as much of the air out as possible to prevent freezer burn.

  20. 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?

  21. 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?

    1. 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.

  22. 4 stars
    Love your recipes! We’d love them more in our diabetic household if they included nutritional information!

  23. 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.)

    1. 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.

  24. 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.” :)

    1. 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.

    2. 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.

  25. Hello!

    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.

    1. Yes, they always stick for me!!! And I forgot that that is what I did last time, skipped the liners and grease the pan! I wish I had read this last night! On the other hand, I used silicone liners on half and they did not stick.

  26. 5 stars
    Made the blueberry muffins and they are delicious. Of course they’re nowhere near the sweetness of a typical sugar heavy muffin. But, for once, I can actually taste the blueberry goodness! My kids love these as well.

    1. Amy Taylor (comment moderator)

      Hi Sarah. They are fine for up to 3 months in the freezer. I would thaw them overnight in the fridge.

  27. Wondering if I used 1c. Flour and 1/2 c of oat flour, would the Muffins hold up. I am new to other flours besides whole wheat. I just know oat flour is so good for you.

  28. Anyone use this to make a savory muffin for snack or lunch/dinner? I’m thinking cheese, spinach (because we could always use more greens), broccoli bits…you get the idea! Just wondered before I start experimenting with food.

    1. Amy Taylor (comment moderator)

      Hi Melissa. You can use frozen blueberries, too. I do let them defrost somewhat but if they are fully defrosted, they may break up as you mix them in.

  29. I just made these with canola oil b/c my husband doesn’t like coconut (they are really really good, by the way) but I would obviously like to not use the processed oils. Could you use melted or unmelted butter?