Oh 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!
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Whole-Wheat Muffins
Ingredients
- 1 1/2 cups whole-wheat flour (I used King Arthur’s white whole-wheat flour)
- 1/2 teaspoon salt
- 2 teaspoons baking powder
- 1/4 teaspoon cinnamon
- 1/8 teaspoon nutmeg
- 2 eggs
- 2 tablespoons honey
- 1 teaspoon pure vanilla extract
- 1/4 cup oil (I used coconut oil)
- 3/4 cup orange juice or apple juice
- About 1 cup of total filling (berries, fruit, nuts, etc. – see below for details)
- Muffin/Cupcake liners
Directions
Heat oven to 400 degrees F. In a large bowl with a fork or whisk mix the flour, salt, baking powder, cinnamon and nutmeg. 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. 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.
Line a muffin pan with liners and fill 2/3 to 3/4 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 1/4 to 1/2 teaspoon of zest per individual muffin)
- a mix of dried fruit bits
- jelly
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. Enjoy!
Yield: 12 muffins

Do you think it’d be better for me to use regular whole wheat flour or whole wheat pastry flour to make these? I have tried the white wheat with other recipes and ended up with a bad bitter flavor
You could try any of those flours and see what you like the best. Also, be sure to keep your whole-wheat flour in the fridge or freezer otherwise it will spoil.
I made these on Wednesday with flax instead of egg and I used pureed pumkin and they were excellent! Thanks!
Is it flax meal that you use to replace the egg? I just bought some on a whim the other day and would love to do some replacing here and there (leaning towards a hypoallergenic diet with my son, gradually)
I followed exactly except for the oil (I used what I had on hand, *unmentionable refined oil*). They turned out with a texture similar to bread pudding, dense – not exactly unpleasant, but not like the lovely muffins in your picture. I will try the recipe again sometime – thank you for this resource!
Making these right now. A few with cinnamon applesauce, some with raisins and the others chocolate chips. My girls don’t go crazy with fruit hidden in things but add choco chips and they will devour them….will make sure to have fruit WITH it in the am though!
2 questions: Do you heat your coco oil first so it’s liquid? I did not and had lumps of it in my batter. Hoping it’ll turn out fine.
Next, any idea with flour substitutions? Am wanting to slowly move us more gluten free over time and wondering what kinds of flours I can sneak in that would give a similar texture? Even just doing a half and half thing for now to ease us over would be fine. Thoughts?
Hm, mine totally stuck to the liners…what’s the trick? Also, taste a bit too coconutty but I guess that’s probably bc of the chunks left in the batter. Otherwise they are nice and soft. Turns out to be a good after school snack…8 yr old is on her second muffin (they are so small anyways since most are sticking to the liner).
You def have to heat the oil. Only a few seconds will do it. I always oil my liners. I use the silicone baking cups.
They could be sticking so much because of the oil being in chunks. They might stick a little, but not half the muffin like it sounds.
Here is a post all about coconut oil (it can be tricky!): http://www.100daysofrealfood.com/2012/02/07/how-to-cook-with-coconut-oil/ And for gluten-free ideas check out Deliciously Organic and Elana’s Pantry.
Lisa, thank you for the work you do encouraging us to eat whole foods. Your website has been a real blessing to my family, and I’m constantly sending links to your blog to friends. Anywho…
My three year old daughter wanted to make muffins, so this was the first place I looked. I thought, surely 100 days of real food has *something* practical and yummy. Score! Most muffin recipes have an obscene amount of sugar, which is why I rarely make them. These were delicious with the orange juice and cinnamon. Such a nice flavor combination. I let my two older kids add their own stuff (6 year old chose chocolate chips, three year old chose raisins?!) , my ten month old is eating hers plain, and I spread honey butter on mine. This recipe is getting printed and put in my cookbook!
PS: I’m apparently not giving the baby her muffin bites fast enough. She’s really honked off about that! And, she’s on muffin #3.
I just made these, the “longer” way. I put in mashed up bananas and blueberries. They are so yummy! Perfect to take away this weekend for our breakfast. I know these are going to be a hit with the kids.
Thanks for another great recipe.
Ok, update on the next day. Kids would not eat them. Said they didn’t taste good anymore. Anyone else run into this? Why would that be?
How did you store them…in the fridge or on the counter?
Counter. Bad choice?
No, that’s what I would recommend for the first couple days. If it was fridge I would say it could have been the different consistency. My girls sometimes love our dinner then won’t eat it leftover the next day. They love to keep me guessing!
Hello! I love your website, thank you for taking the time and effort to put all of this together and making it public for anyone to read. Fantastic! I do have one question though. My roommates and I make a recipe called “primal pizza” every once in a while, but instead of using normal pizza dough, they use ‘Almond Meal’ (which we buy from trader joes), mixed with egg and olive oil. I am wondering if you could replace flour with almond meal in certain recipes. It does say on the label that it can be substituted for up to 50% of the volume of flour called for in recipes, however the final product might not hold together so well. It works for our pizza and tastes great, (though I usually eat pizza with a fork, so for others, it might not be the best) What are your thoughts?
Anytime you start making substitutions it definitely becomes an experiment…but almond meal is a great “whole food” choice if you can get it to work!
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I’ve made these a few times now and we absolutely LOVE them. I’m having a bit of a problem with the muffins really sticking to the muffin cups. I don’t really want to use a cooking spray on them but I don’t know what else to do… any suggestions?
You could try silicone muffin liners to see if you have better luck…and maybe brush them with melted butter. Hope that helps!
I made these today and they are delicious! I actually used Spelt flour and they came out great. I used mashed banana and walnuts and apple juice instead of orange. Yum! Thanks!
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Love these muffins! Thank you for the recipe. They have turned out great each time!
I made these (blueberry) this afternoon and while they taste yummo (will be a nice dessert this evening with a touch of whipped cream!) they do, indeed, stick to the liners. I think in the future I’ll forego liners entirely (i don’t care for the silicone liners, as I think they are way more trouble than they’re worth with cleaning them) and merely brush the muffins pan holes with a bit of butter. But tasty, nonetheless, just not “easy” to dole out when Mom has to peel the liner off and scrape the bottom of the muffin off the liner to also give to the kiddo. LOL
Just made these, followed the recipe exactly and used OJ and blueberries. These may have been the driest muffins we’ve ever eaten. My kids did not like them, said they needed water. I’d use applesauce in place of the eggs and add maple syrup instead of the honey in a higher quantity next time. Think I’ll stick to my vegan muffin recipes