Whole Wheat Lemon Raspberry Muffins

75 Reviews / 4.9 Average
The raspberries and lemon in this recipe complement each other so well. I hope your kids gobble up these whole-wheat lemon raspberry muffins like mine did. Make sure to bake a second batch to freeze for later.
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I am in love with this new recipe for whole wheat lemon raspberry muffins! It’s so good I think I want one with frosting on top for my birthday (which is not until May, but a girl can plan ahead)! The raspberries and lemon complement each other so well, and it’s such a nice diversion from the usual muffin flavors. You will also love this Raspberry Bread!

Whole-Wheat Lemon Raspberry Muffins from 100 Days of #RealFood

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Lemon raspberry muffins with whole wheat flour and real food ingredients

These flavor-packed lemon raspberry muffins are made with whole wheat flour and have no refined sugar. I always advocate eating real food, and leaving out the processed ingredients really brings out the natural flavors of the fresh lemon zest and raspberries in this muffin recipe. Check out these red fruits too!

Instead of sugar, I used ½ cup of pure maple syrup to balance out the tartness of the raspberry and lemon. You can easily substitute the sugar with other natural sweeteners such as honey or applesauce, but I find the maple flavor compliments the fruit flavors perfectly.

Learn all about the different types of berries!

How to use fresh or frozen raspberries in these lemon raspberry muffins

I love baking with frozen raspberries! Since they’re preserved immediately after picking, frozen raspberries can actually be more flavorful than the fresh ones you buy at the store. Frozen berries are also a great way to eat real food on a budget.

The downside to frozen raspberries is that they can become mushy very quickly, which means instead of delicious chunks of raspberry in your muffins you wind up with lemon and raspberry flavored muffins (and dyed batter). To avoid this, leave your raspberries in the freezer until you’re ready to use them. Once you add the berries, don’t let them warm up while you fold them into the batter or fill your muffin pan.

If you prefer using fresh raspberries you don’t need to worry about thawing, but you should still make sure to fold gently since raspberries, especially ripe ones, mash easily.

How to zest a lemon

The fresh lemon zest is what adds the lemon flavor in these lemon raspberry muffins! If you’ve never zested a lemon before, you’re essentially just grating the peel with a fine grater. I recommend using a microplane (over a zester) for the best texture.

To zest, first clean and dry your lemon. Then place the end of your microplane on the cutting board, holding it with one hand on an angle. With the other hand, run the lemon back and forth on the microplane; the grated lemon will fall on the cutting board below.

  • Don’t grate the white part of the lemon peel. This part is bitter on all citrus fruit.
  • You only need a small amount of lemon zest; adding too much can overpower the raspberry flavor in these muffins.
  • Be gentle as you zest and don’t press down too firmly.
  • The microplane is VERY sharp so be careful not to slip and cut your hand or fingers!

If you don’t have a lemon zester or microplane you can also use a box grater or cheese grater. Choose the smallest size option and then run the lemon back and forth until you have 1 teaspoon of zest.

For more baking resources, check out this Teaspoons and Tablespoons guide. Use the zest in our Lemon Blueberry Bread!

Can I use lemon juice instead of lemon zest?

Lemon zest and lemon juice have slightly different flavors and levels of acidity, but if lemon zest isn’t an option, 100% freshly squeezed lemon juice will work in a pinch.

To substitute the lemon zest with lemon juice in these lemon raspberry muffins, first skip the step where you add zest. Then add 2 tablespoons of lemon juice with the other wet ingredients.

Lemon juice can sometimes taste more tart than zest, but you probably won’t notice a huge difference in this muffin recipe because there are so many other flavors to balance it out.

How to store whole wheat lemon raspberry muffins

Cooled leftover muffins (if you even have any leftovers!) can be stored in an airtight container at room temperature for 1-2 days, or in the fridge for up to 1 week.

Muffins can also be frozen for up to 3 months. Thaw at room temperature, in the fridge, or in the microwave for a quick, healthy snack or grab and go breakfast.

I hope your kids gobble up these lemon raspberry muffins like mine did. I’d love to hear what they think in the comments below. :)

Other muffin recipes you might like

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Recipe Rating




  1. These are my favorite muffins by far. I’ve made them for friends and they love them just as much.
    One question though: how much butter is too much? It seems like a lot for the recipe, but of course it is real food and it comes out moist and scrumptious. Let me know your view on limits of butter usage. Thanks! I am using your recipes all week long and have really been loving the variety and feeling good about knowing everything that is in my family’s food.

  2. 5 stars
    Wow. Just made these and just wow! Absolutely delicious!! Made the recipe as stated except I used my mini muffin pan. They only took right at 13 minutes to be cooked to perfection.

  3. I made these for my girls and husband for Valentine’s Day breakfast. They were excellent! Not too sweet but just right. Love the recipe, thanks for making our real food journey of five years and counting so much more enjoyable!!!

  4. I used this recipe to make 100 mini muffins for my daughter’s 100th day of school party. I tripled the recipe and baked in a mini muffin tin for 15 minutes.

  5. 5 stars
    These muffins are SO good!! I usually make muffins with an oil, typically coconut oil. I think the butter really made all the difference in flavor and texture in this recipe. We have an egg allergy, so I made these with about 4 oz of applesauce to replace the egg and they are perfect.

  6. I made these muffins with orange zest and cranberries. (I had fresh cranberries that needed to be used.) Very good, although I think I’d prefer a bit more orange flavor. Maybe next time I’ll try subbing some orange juice for some of the milk, although I’m worried the acidity will react with the milk. I can’t wait to try the lemon-raspberry combo!

  7. Rhonda R. Hudgins

    I absolutely cannot even tolerate the smell, let alone the taste of Maple Syrup [I know I’m strange, but it just …] what can I use instead? I really would love to try these.

  8. 5 stars
    I love these muffins! They are fabulous! I usually split the flour in two- 1/2 whole wheat and the other 1/2 white

  9. 5 stars
    What?? These are healthy muffins?!? They are way too delicious to be healthy!! I have made these a few times and they turned out great! The second time making them I doubled the lemon zest and used blueberries instead of raspberries (cause it’s all I had on hand!). Super. Yum.

    1. Amy Taylor (comment moderator)

      Hi Shannon. Sure, but keep in mind that chia will gel when combined with liquids and can change the texture of the muffin.

  10. These muffins are absolutely delicious! The only reason I gave a 4/5 is because I don’t think the butter is necessary. Instead, I added 1/2 cup of applesauce and they couldn’t have been more moist. And healthy! This is a keeper

  11. These are the best muffins in our rotation! We make the recipe at least once a month but sometimes more! My toddler thanks you!

  12. Awesomely, amazing muffins! My whole family sat down to eat one as they came out of the oven and they all wanted another one. They are really moist, lightly sweet and very addictive!

    1. Amy Taylor (comment moderator)

      Hi there. You can replace the butter 1:1 with coconut oil and some readers have used applesauce in its place, as well.

  13. Mmm! I made these today, but used frozen dark cherries instead of the berries. I also drizzled a little maple syrup on top to give it that “wow! treat!” factor for the kids, who are being weaned off regular muffins/cupcakes. They were a hit! New favorite recipe, thank you!

  14. I don’t have frozen raspberries, I have about a cup of fresh berries. I don’t want them to go bad, and I’ve looked at this recipe quite a few times, and really want to try it. What changes do I have to make to use fresh instead of frozen. My freezer is too full to lay them out on a cookie sheet and freeze them.

  15. Awesome! I only had some frozen blueberries, so I substituted those for raspberries. Also, I use “cup for cup” gluten free flour :))) So good, but now not sure which are my faves these or the pumpkin spice ones.

  16. Amy Taylor (comment moderator)

    Hi there. Here are our terms of use: https://www.100daysofrealfood.com/terms-of-use/ for your reference.

    Specifically: Sharing Recipes Online

    If you wish to share one of our recipes, write your own introduction (or review) and then provide credit and a link to the original recipe. A mere list of ingredients is not copyright protected, but the creative, expressive content and words of the recipe are.
    If you make slight changes to a recipe, it’s still someone else’s recipe. The guidelines are the same as in #1 above, but of course you may add your additional comments to highlight the changes.
    If you adapt a recipe and do in fact make significant modifications, you can publish your version (the entire recipe) but you need to give credit and a link back to the source (if available online).

    See this page for an example of how we handled this for a recipe we adapted: https://www.100daysofrealfood.com/2011/08/01/recipe-pork-carnitas-tacos-with-tomatillo-salsa/.
    :) ~Amy

  17. 5 stars
    I love these! They’re a huge hit with my friends at college. I’ve made them once and my roommate has already asked for the recipe! I wanted to check and see if it’s alright if I enter your recipe into livestrong.com so that I can track my calories with it. I have the option to keep the recipe private if you’d prefer that, otherwise if I do make it public I can include the link to this page in the recipe and just say “adapted with permission from:” followed by the link (or something along those lines. Just let me know! Thanks!

  18. 5 stars
    Yummy! It was a hit with everyone! I added the juice from a home grown lemon and organic syrup instead of pure maple syrup.

  19. Carolyn VanOstran

    5 stars
    Made these today using almond milk in place of the milk. I was a little worried when the wet ingredients didn’t blend together well, but after adding the dry ingredients, all was well. They turned out delicious!!!!! Will definitely be making these again.

  20. I just made them this morning and they taste great but they came out looking a little green. Is this normal or did I make a mistake. Has anyone else noticed this and are they ok to eat? I used Trader Joe’s Whole Wheat flour and real maple agave plus everything else mentioned in the recipe.

    1. Amy Taylor (comment moderator)

      Hi Michelle. It was probably a chemical reaction between some of your ingredients. Baking soda can react that way with some fruits but it is not harmful. ~Amy

    2. Mine turned green too with the raspberries. They taste good though. I have made these before with a small can of pineapple chunks and they didn’t turn green.

  21. Just made these tonight. Took a little longer to cook, but my daughter couldn’t wait to try them. Rave reviews. Will definitely do this again–even double the recipe.

    1. Amy Taylor (comment moderator)

      Hi there. We’ve never tried. FYI, Costco and Trader Joes has great prices on their real maple syrup…no corn syrup. ;) ~Amy

  22. I have a dairy allergy so could I substitute grassfed Ghee for the butter and almond milk for the milk? These sound delicious!

    1. Carolann – I saw in one of the earlier comments that someone used 2 tablespoons of lemon juice instead of the zest and she loved them. Haven’t tried myself yet but am going to!