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 and these Chocolate Raspberry Muffins!

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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
- Whole Wheat Banana (Nut) Muffins
- Whole Wheat Carrot Applesauce Muffins
- Apple Walnut Muffins
- Blueberry, Fruit, Nut (or anything you want) Whole Wheat Muffins
Patty says
Do you have the nutritional value for these? I'm trying to follow a 1200 calorie diabetic diet.
Thanks so much
Amy Taylor (comment moderator) says
Hi Patty. We do not provide nutrition information. This will help explain why: https://www.100daysofrealfood.com/2013/01/04/healthy-eating-defined/. Can I recommend a website for you? Dr. Mark Hyman is my guru of functional medicine and you might find his info very helpful: http://drhyman.com/blog/2012/03/01/cure-for-diabetes-discovered/. ~Amy
Shiri says
Could I use coconut sugar instead of maple syrup?
Amy Taylor (comment moderator) says
Hi Shiri. We've not tried. It is not quite as simple as just switching them out because one is wet and one it dry. Let us know if you experiment. ~Amy
Cindy says
Can I substitute spelt flour for the whole wheat? If so, would it be a straight 1-for-1 substitution?
Thanks!
Amy Taylor (comment moderator) says
Hi Cindy. 1:1 should work fine in this recipe. :)
Kim says
I have made these twice now! The first time I just subbed a flax egg for a normal egg, and used a combo of frozen blueberries & raspberries. So good!!! perfect amount of lemon & sweetness. The second time I made them I didn't have any maple syrup so I subbed honey. They were still good but but I definitely prefer the taste with maple syrup much better! I also didn't have enough butter so I did 1/4 butter & 1/4 cup coconut oil. They were super moist. Moral of the story: stick with maple syrup for this one :-) Thanks for another great recipe!! Love that they freeze well also!
Kathy says
The raspberries are too tart for my personal taste. I used blueberries instead. Delicious and they do freeze beautifully!
brooke says
Can you substitute rolled oats for flour?
Amy Taylor (comment moderator) says
Hi Brooke. This might help: http://www.livestrong.com/article/557742-baking-with-oat-flour-vs-wheat-flour/. ~AMy
DC-NoVa says
This is by far the most versatile recipe I've ever had! I love it--thank you!! I have swapped OJ for the milk, honey for maple syrup, cranberries (Craisins) for the raspberries...and it's always excellent. I've done lemon blueberry and pumpkin, too, and only added cinnamon and/or nutmeg. Thank you for a great recipe that can take the abuse!
Kelly says
How did you add in the pumpkin?
Thanks
DC-NoVa says
I omitted the lemon and berries, swapped honey for the maple syrup, used an entire can of pumpkin, added about 3/4 cup of Craisins, 1 Tbsp of cinnamon with 1/4 tsp nutmeg and a pinch of cloves. I mix the wet in one bowl and the dry in another, then combine them. I usually don't use milk, either (if I need the moisture, I'll use a single serve container of applesauce in the milk's place). But the pumpkin is fine without the applesauce because it's so moist (but you can keep the milk out until you mix both bowls together, in case it needs the wetness). And salted butter is better than unsalted for flavor. Hope that helps! :)
Jaimie says
Do these freeze well? Baking my first batch now!
Amy Taylor (comment moderator) says
Hi Jaimie. They do! :)
Shannon says
Is there a suggestion for egg free for this and the other muffin recipes (my son is allergic).
Amy Taylor (comment moderator) says
Hi Shannon. Lots of readers sub with flax eggs. Here ya go: http://www.veganbaking.net/recipes/egg-replacers/flax-seed-egg-replacer. ~Amy
Martha says
Will it be ok if I use lime instead of lemon?
Amy Taylor (comment moderator) says
Hi Martha. Yep, should work fine. :)
Liz S says
We love these! I'm going to make some today with poppy seeds instead of raspberries...can't wait to try them!
Liz S says
They turned out amazing!!! Followed your recipe exactly, but instead of raspberries at the end, I added 2TBSP of poppy seeds. They are delicious!
Marla says
I made these today with my two daughters to freeze for back to school. Of course we had to try just one and the results were outstanding! Loved by all! Next time I'm going to double the recipe 😀
Nicole says
I subbed honey because I was out of maple syrup. I also chopped up some fresh rosemary and added it to the batter. Delicious and the kids love them! Thanks
Michelle says
I made a coconut version of these tonight. I used coconut oil instead of butter (I whipped it together with the eggs), 1/4 C of unsweetened coconut and 1/4 cup buttermilk (because it seemed thick) and they were delicious! Mini muffins cooked in about 12 mins.
Erin says
Would frozen blueberries work?
Assistant to 100 Days (Amy) says
Hi Erin. Yes, they will. :)
lauren says
can you use whole wheat WHITE flour??? I don't know the difference
Assistant to 100 Days (Amy) says
Hello Lauren. Yes, whole white wheat is still 100% whole grain. It is just a "lighter" colored wheat berry. ~Amy
Heidi says
I'd like to make these into mini muffins--how long should I bake them if I use a mini muffin tin?
Thanks!
Assistant to 100 Days (Amy) says
Hi there. Start checking them around 12 minutes. :)
Amy says
I made, I loved, I made again! I used silicone muffin wrappers - filled them about 1/2 way and it made 14 muffins. Thanks for the recipe!
Amanda says
I made these this evening and the outsides were done and most of the inside, but it was pretty soggy around the berries. Did I do something wrong or is this typical?
Assistant to 100 Days (Amy) says
Hi Amanda. The muffins will be more more moist around the berries but the muffin itself should not be "soggy". ~Amy
Janice says
Hello- do you have the nutritional info for
your raspberry muffins please?
Thanks!
Assistant to 100 Days (Amy) says
Hi there, Janice. We do not provide nutrition information. Our focus is on getting real food into people's lives and we've found that calorie counting becomes unnecessary when incorporating mostly whole/real foods into your diet. There are plenty of online tools that can calculate all details for you, however. Many readers like My Fitness Pal. ~Amy
Lauren says
Hi,
I was wondering if I could substitute almond milk? Thanks!
Heidi says
Lauren, I substituted almond milk when I made these last week and they came out perfectly!
Vicki Luciano says
So, you can use fresh raspberries? Do you still use the same amount of fresh raspberries as frozen raspberries?
Assistant to 100 Days (Amy) says
Same. :)
Darcie says
I just made these (with some minor adaptations), and they turned out pretty awesome! Thanks for the recipe; I had been hunting for a raspberry muffin recipe for awhile. :)
Jennie says
I adjusted the recipe for high altitude decreasing baking soda to 3/4 tsp, used buttermilk and added a TBLS. more, added 1 TBLS of flour. Also used fresh raspberries and poured into 6 jumbo silicone cups and baked for 26 min.
Perfect and delicious!!
Erin says
This is a great recipe to keep on hand. Very easy to make. I ran out of syrup so I did half syrup and half honey which worked just fine. I also didn't have raspberries so I used some diced up peaches I had in the fridge and the muffins were AMAZING! easy grab and go snack or breakfast item.
Cora says
Oh My Stars...these are DELICIOUS!!! Easy and oh so good! And very moist too!
Cassandra says
Holy cow, these are amazing! II tried one while it was still warm and was amazed at how yummy they are...my new favorite muffin recipe.
KK says
I just made these with a few substitutions and they are amazing. We live in Thailand, where maple syrup is an expensive luxury, so I substituted 2 finger bananas for 1/4 cup maple syrup. I also used buttermilk instead of regular milk, and substituted half of the butter for coconut oil. Frozen raspberries are also very expensive here, so I used chopped up frozen strawberries. The muffins are light, fluffy and delicious. I can wait for my husband and 3 year old to try them.
Trish says
How do you store these muffins? In the fridge or just on the counter. I don't think they will last long, but just wondering. Thanks!!
Assistant to 100 Days (Amy) says
Hi Trish. Freeze them for the longest life. They will be okay in a airtight container in the fridge for a few days. ~Amy
Melinda says
Turned out delicious! I had to sub coconut oil for butter, soy milk for milk, and did a mix of blueberries and raspberries (all I had on hand) and it turned out great. Very moist and flavorful.
Renee says
Have you ever tried making these with coconut flour? I have a hard time digesting grains. If so, would you measure out the same amount of coconut flour?
Assistant to 100 Days (Amy) says
Hi there. I have not used coconut flour for this recipe but it would not be a one to one conversion. Coconut flour soaks up a great deal more liquid. ~Amy
Jamie says
These were so delicious!!! My kids absolutely loved them. Thank you for sharing this with us.
Abbey says
Hi! How long do these muffins stay fresh if you keep them in the fridge?
Assistant to 100 Days (Amy) says
Hi Abbey. I usually freeze these to keep them freshest but they should be okay in an airtight container in the fridge for several days. Refrigeration can dry them out, however. ~Amy
Karen says
I love the taste of these but every time I make them they crumble to piece immediately and don't hold muffin shape. Any ideas?
Assistant to 100 Days (Amy) says
Hello. Whole wheat has less gluten which might be responsible for a texture you aren't quite used to. Try adding just a little chia to the wet ingredients to help bind the ingredients. :)
Kelly says
My kids won't eat the thicker more dense bread from using whole wheat. Could I do half whole wheat flour and half white?
Amy K says
I haven't made this recipe yet, but I typically use white whole wheat flour since it seems to bake up less dense than regular whole wheat.
Katy says
You can also use whole-wheat pastry flour, which is finer than regular whole-wheat flour. I use it all the time, for everything.
Erin says
Hello, could I substitute blueberries for raspberries in the raspberry lemon muffin recipe? Thank you!
Christy says
I have made this with both raspberries and blackberries..my husband who has been a little harder to get on board with healthier eating LOVES them both ways!! I bet substituting with blueberries would also turn out great!
Denise says
I really want to try these as we just picked a ton of fresh raspberries but I don't have a lemon, do you think orange zest would taste just as yummy?
Assistant to 100 Days (Amy) says
Hello Denise. I've subbed orange zest in other recipes in a pinch. I think it will work with a bit different flavor, obviously. ~Amy
Julie says
Thanks. I think I will try the honey instead.
Heather says
Have you tried these with fresh raspberries? Also, how would honey be in replace of the syrup? They look yummy. I love your site!
Assistant to 100 Days (Amy) says
Hi there. You can certainly use fresh raspberries but they will break up when you mix them in. The taste will be fine, though. You can also use honey in place of the maple syrup for similar results. :) ~Amy
Julie says
Is syrup really healthy? What is it replacing....sugar? Does it have to be pure?
Assistant to 100 Days (Amy) says
Hi Julie. Lisa avoids refined sugars in most of her recipes and opts for more natural honey and pure maple syrup. ~Amy