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

I am in love with this new recipe for whole wheat lemon raspberry muffins! It’s soooo 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 compliment each other so well, and it’s such a nice diversion from the usual muffin flavors.

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.

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.

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 micropllane 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.

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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374 thoughts on “Whole Wheat Lemon Raspberry Muffins”

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Recipe Rating




      1. Hi Melissa, sorry we can’t respond back in real-time, but you can put them in the fridge or in an airtight container on the counter. – Nicole

  1. 4 stars
    Made these a few days ago – veganized it by using almond milk, vegan margarine and a flax “egg”. Mine ended up a lot flatter than yours, not sure if the veganizing caused that but no big fuss as they still tasted great. Love how hearty they are while still being moist, the last few wholewheat muffins I’ve tried to make end up like hockey pucks. Also appreciated the different flavour, usually I lean towards chocolate so this was a nice change, thanks for a great recipe!

  2. Tried this tonight with blackberries – super delicious! Might add a touch of lemon juice next time for a little more lemony goodness.

  3. 5 stars
    Wonderful recipe! I’ve tried the original recipe along with different variations (with fresh raspberries, frozen blueberries, fresh blueberries and King Arthur White Whole Wheat Four). We are going to try the recipe with strawberries today! Agree with some of the other comments that the mixture of butter, egg, maple syrup, milk and vanilla can look a little clumpy. I have brought all the ingredients to room temp and while the consistency does improve a bit, it still looks clumpy. However, I now do not give it a second thought because the end product is fantastic. Another great recipe! Thanks. :-)

  4. Love the texture and flavor. I used blueberries since that’s what I. had on hand. Will definitely make these again.

  5. Thank you so much for this recipe! I made a double batch today with blueberries instead of the raspberries. Also, I did half honey and half maple syrup for the sweetener. My whole family loved them!

  6. 5 stars
    My daughter, husband, and I loved these! The butter mixture didn’t initially blend super well but it all came together nicely when we added the flour mixture.

  7. 5 stars
    My new favorite breakfast! One of these muffins with some fruit will keep me full and satisfied for quite awhile. (Unlike muffins made with fake ingredients which just leave you craving something else to eat.)
    They freeze wonderfully and are the perfect thing to pop in the microwave for 40 seconds and enjoy with a cup of coffee!

    1. Amy Taylor (comment moderator)

      It helps to have your other wet ingredients at room temperature. I typically let the eggs and milk sit for a bit.

  8. Another great recipe of yours! Made these in the waffler iron, per your 4 Fun Things to Try in the Waffle Iron! They were great and made for a delicious tea party!

  9. I made Thea for breakfast this morning and they pretty much disappeared. I used whole wheat pastry flour and buttermilk. They were AWESOME!!! Thanks for a great recipe

  10. 5 stars
    My 10 year old made these but with frozen blueberries that we froze from when we went blueberry picking. I was so surprised how yummy these are! We are new to whole wheat flour and I was little nervous about the taste but we were not disappointed…made them last night and only 2 left! Thank you for the recipe, I originally saw it in the second book And my 10 year old needed to bake asap ☺️

  11. 5 stars
    I just need to comment on how fabulous this recipe is. I’ve now made them over a dozen times as is and with variations. I’ve replaced the raspberries with blueberries, I’ve also used strawberries along with cinnamon instead of the lemon. Just such a versatile recipe! Thank you!

  12. I made these for my family this morning. We loved them! So delicious. I actually substituted raspberry for blueberries. Will definitely make these again.

  13. 5 stars
    These are unbelievable! So delicious and the perfect texture. I added a whole bag (10oz) of frozen raspberries because I love them, and it same out very well-bursting with raspberry lemon flavor. Do you think it would be possible to replace the butter with equal volume coconut oil?

  14. What can I sub for the milk? I’m working at removing dairy for a while and am not a fan of soy or almond milk. Could coconut water work?

  15. 5 stars
    I LOVE lemon & raspberry, so I had to try these. I did sub unsweetened applesauce & full fat plain yogurt for the butter, since I needed the butter in another recipe. They were delicious!

  16. 5 stars
    I LOVE this recipe! Fun modification, I replaced the butter and lemon zest with Zesty Lemon Grapeseed Oil from Wildtree. Friends were blow away how much lemon flavor came just from oil. And the grape seed oil is healthier than butter. Plus I didn’t have to get my hand mixer out. Nice!

    1. Great idea. Did you use the same amount of oil or reduce the amount? What was your ratio? Thanks for sharing. I’m eager to try a dairy free version!

  17. Made these with my 3YO son and they were a hit! Does anyone know where I can find the nutrition facts on these? Just wondering how many grams of sugar (approx) are in each muffin. Thanks!

    1. My maple syrup has 53 grams of sugar per quarter cup, and the recipe calls for a half cup of syrup, so that makes 106 grams per batch. A cup of raspberries adds 9 more grams of sugar, bringing the total to 115 grams of sugar per batch. Divide that by 12 muffins, and you get about 9.6 grams of sugar per muffin. I would check your ingredients (maybe the sugar content is different in your maple syrup), but it’s probably pretty close.

      1. Ooh – plus another 6 grams of sugar per half cup of milk, so 121 grams per batch equals closer to 10 grams per muffin if I’m not forgetting anything else!

  18. 5 stars
    My 2y/o, 1y/o, husband, and I LOVED these for breakfast this morning! I used frozen blueberries just b/c that’s what I had in the freezer :-) They were sweet and moist!

  19. Any substitute for the pure maple syrup? We live overseas and don’t have it here. Also, our equivalent of raspberries are super tart and require something to sweeten then. I wondered about honey in place of the syrup, but not sure how much to use.

    1. Cindy, I would use honey in a 1:1 sub. You could use blueberries or chopped up strawberries instead of the raspberries.

  20. Just a tip for those who are thinking of substituting coconut oil for the butter: don’t. When I added the frozen raspberries, the whole batter froze up! I still managed to get them into the muffin tins and baked, but it was a pain to work with.

  21. 5 stars
    Made these with my 3 year old yesterday and they are amazing. We both ate two each right after they came out of the oven. Thanks for the wonderful and simple recipe.

  22. 5 stars
    I love these muffins! I’m wondering how you defrost them (and any muffins) without them becoming soggy. Any tips?

    1. Amy Taylor (comment moderator)

      Hi. You can defrost on the counter or in the fridge. I’ve not had problems with excess moisture. If you do, you can throw then in the oven for a bit to reheat.

  23. 5 stars
    My kids and I made these today. We used whole grain spelt flour, which I usually like better than wheat flour for baked goods. We also used fresh raspberries and made them into mini-muffins, which took about 10 minutes. I should have used liners but we were out of them, so they did stick a little because of the gooey raspberries. But, they still tasted SO good, and all the kids loved them! Yum!

  24. 5 stars
    Wow– soooo, so good! These are fabulous. Made them exactly as the recipe calls. Perfect. Wondering if theres a way to bump up the protein or fiber?

  25. 5 stars
    Made these to go with my Father’s Day brunch yesterday and they were a huge hit! Definitely your best muffin recipe!

  26. These sound delicious. Any recommendations for how to replace maple syrup with coconut sugar? Our maple syrup is precious…(c:

  27. I love these muffins! I have made them a few times and can hardly resist eating several. My only concern is the Amt of butter. Seems like a lot of greasiness on my muffin papers at the bottom when I put them
    On a rack to cool. Has anyone else experienced this? Is there replacement for part of the butter?

  28. 5 stars
    These are fantastic!! I used fresh raspberries, folded in, and I added one or two on top just before baking. And I used 1/4 cup syrup and 1/4 cup honey. They are perfect! Thank you!!

    1. Amy Taylor (comment moderator)

      Hi. That’s not something we’ve tried. You might need to add a little more wet ingredients if add dry ingredients.