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






Danielle says
Wow! I made these last night as an after dinner snack and they were AMAZING! My husband and 3 year old enjoyed them too. My daughter did say she still likes the pumpkin muffins and carrot/applesauce muffins better, but these are my personal new favorite :)
CJ says
I made these today and they turned out delicious! I used whole spelt flour instead of whole wheat and, due to my daughter's allergies, I used the flax egg substitute in place of the egg (1 TBSP ground flax + 3 TBSP warm water). Thanks for another awesome recipe and for all that you do! :)
Kristen says
I made these today and they were delicious! I also was low on maple so used 1/4c maple and 1/4 c unrefined coconut sugar and I used buttermilk instead of whole milk since I had some. Yum! Very light and moist. I was slightly shy on raspberries so made two with blueberries and they are yummy too! I liked the carrot applesauce ones but my 6yo (who LOVES carrots) did not. Can't please everyone all the time!
Jan Moran says
Love these, Lisa! I'm an author, and we always need healthy fuel to stave away the snack monster. I'm not waiting until my birthday (also in May) either!
Jen says
Love these!!! I made these last night using frozen blueberries and almond milk. They were super tasty, but higher in calories than I want. So I made them again today still using frozen blueberries and almond milk but I used unsweetened applesauce instead of butter. Still very yummy and clean, but minus several calories.
Roanna says
Mine came out super dry. I used fresh strawberries instead of any othertype of frozen fruit.
Could that have altered the moisture factor?
Kelley says
Since you used fresh strawberries instead of frozen raspberries you probably overcooked the muffins. Next time shorten the cooking time and I'm sure they will turn out great.
Courtney says
I made these last night and they are delicious. The only change I did was using 1/4 cup of maple syrup and 1/4 of sugar because I didn't have enough maple syrup. I know, I know, sugar is bad bad bad, but 1/4 cup for 12 muffins isn't too terrible. Next time I will try the recipe as written.
Stacie says
These were amazing!! I couldn't zest my lemon, so I just juiced half of a lemon instead. They were awesome! Going to make a double batch today just for the freezer :)
Ashley says
Do the berries have to be frozen? Could you use fresh?
Assistant to 100 Days (Amy) says
Hi Ashley. You can certainly use fresh. :) ~Amy
Cheryl S. says
Made them!! Awesome! Delicious. Two thumbs up from kiddos!
Laura says
I have made several of the muffin recipes and my 5 year old just doesn't like them. I was hoping to make muffins and the granola for an easy breakfast each week for our family. My husband and I love the muffins, but my daughter doesn't think they are sweet enough. Any suggestions or changes to the recipes that could help?
Brittany says
Laura,
My 3 year old finally ate her first whole carrot applesauce muffin today instead of just kind of playing and mushing it around. I have always given her some with the other kids knowing it was probably going to be wasted, which I hate, but also want to give her a chance. So patience does pay off!
My oldest daughter doesn't like banana bread all that much because it isn't sweet enough for her. If you use liquid stevia at all that may be an option. I recommend Nunaturals brand. It only takes a tiny bit. I think 1/4 tsp equals one cup of sugar sweetness equivalent (could be wrong so google it) so I will add that when I make it and she loves it now.
Also, sometimes you just keep trying and patience and time will help. I made tomato soup for my kids the other day. We used to regularly each campbell's condensed- yuck, I know. At first they could barely choke down the homemade because it was different and not as sweet. This last time (and I hadn't made it for about 6 months) they raved about how good it was and how much they like it more than the old canned crappy stuff. So maybe a break or just keep trying?
Sometimes you just have to accept some don't like particular foods too. Hard to please all. Some kids will eat granola and one won't touch it. Good luck!!!!
Tess D says
Laura, I would also say be patient. Not sure how much sugar your kids are used to -- sounds like you're in the process of "cleaning up". I know it takes some people a while to adjust a sweet tooth -- it did for me. Lisa's muffin recipes are plenty sweet for me now, but it was an adjustment, especially from storebought and other recipes that had much more sugar. Hang in there! Tastes will change :-)
nicole says
Very Yummy! Made with 1/4 C maple syrup and 1/4 C honey because I ran out of maple syrup. I didn't get a very big lemon flavor so I think I will increase the lemon zest next time but so good will def make again.
Sierra says
Sounds yummy! Perfect for spring. Do you think coconut oil would work instead of butter?
Assistant to 100 Days (Amy) says
Hi Sierra. Yes, I thing coconut oil will work fine. ~Amy
Jennifer swallow says
Great recipe! I can't wait to share it with others.
Haley @Cupcakes and Sunshine says
I have been wanting all things lemon lately. I can NOT wait to try these! Pinned and purchasing ingredients for them :)
renee says
I just made these with lemon juice instead of zest and frozen blueberries. Very yummy. 5 year old gobbled them up.
Tiffany says
Renee, how much lemon juice did you use?
renee says
I substituted 2 Tablespoons lemon juice in place of the zest. I never have lemons in the house when I could use them!
Jessica says
Could I swap the whole wheat flour for almond flour or another flour? And almond milk instead of regular milk? Thanks!!
Assistant to 100 Days (Amy) says
Hello Jessica. Almond flour cannot be subbed 1:1 with whole wheat flour. I'm not sure what the ratio would be and you would also likely need a combination of flours. In most recipes, almond milk does work as a sub for milk. ~Amy
Natasha d says
I sub coconut oil for butter/oil in many recipes! I think it works great!!
laramealor.com says
I love that these lemon zest in them! I also love the lunchbox love cards what a cute idea!
http://www.laramealor.com/new-balance-real-world/
Becky says
I sub organic spelt flour (Bob's Red Mill) for whole wheat (1:1) in recipes like this. I think they turn out a bit lighter and delicious.
Tiffany says
I think I might try these with blueberries since I have a stash in my freezer. When I was a kid my mom put little Suzy's Zoo lunch notes in my lunchbox. They made my day :) I hope to this for my boys when they get a little older.
Kelly says
Well I personally am a fan you have switched me to whole wheat flour I can't wait to make these muffins the carrot applesauce ones were gobbled up by my two toddlers and my husband who wasn't too sure:)
Carol says
Can't wait to try these. Would whole wheat sphelt flour work?
Assistant to 100 Days (Amy) says
Hi there. Spelt should work, too. ~Amy
Amy S. says
I noticed that you use all whole wheat flour. Have you used whole wheat pastry flour and what are your views on it (any health differences)? I've noticed that the pastry flour gives the muffins a lighter consistancy. Thanks!
Assistant to 100 Days (Amy) says
Hi Amy. Whole wheat pastry flour is absolutely fine if it works well for you. It is lower in protein which makes for a lighter end product. ~Amy
Blair @ The Seasoned Mom says
We love muffins, and this looks like the perfect spring recipe. Can't wait to try them!
Courtney @ Family Gone Healthy says
These look awesome! I am a huge fan of lemon so these are right up my alley. I think my daughters and I will be fighting over them.
Danielle says
I highly recommend prairie gold whole wheat flour. I think it's the best out there and is the only flour I've found to be able to use in recipes and not have to use white flour. I love it! I actually prefer it to the King Arthur flour...and it's non GMO too which is awesome. Hope that helps someone. And...can't wait to try these muffins. Thanks for all the great recipes!
Caitlin says
Thanks! I'll try to find that!
Sarah says
There are no GMO wheat's on the market. It's not needed in wheat. What you might be thinking of is hybridized wheat? Everything we eat today has been breed over many generations to make it immune to diseases that will kill the entire crop and lead to mass starvation or yield enough wheat to feed the current population.
Rant over. Yes, that particular brand of wheat is pretty good. I found my bag at Wal-Mart.
Sarah says
You will love the micro plane zester. I use mine ALL of the time (besides spoons and knives it's my most used small appliance). I use it for citrus, parmesan, and I've started grating my garlic. I don't have a press and it's much easier than mincing. Perfect for adding super fine garlic to vinaigrettes and stir fry's.
Kristen says
What a great idea to use the microplane for garlic. I'm stealing it. :-)
Sarah says
Just be careful to not grate your fingers!
Shelly says
I am curious as well about using all wheat flour. I made the whole wheat sandwich bread in the bread machine and it was like a rock. We had to throw the whole load outside.
I know that when I make pizza crust I have to use 3/4 wheat and 1/4 white flour or it has such a heavy texture.
Kristin says
I swap out 100% white whole wheat flour (Trader Joe's brand), for AP flour in all my favorite muffin recipes and they turn out great every time. My kids and husband gobble them up! I do know that the online baking consultants at King Arthur Flour suggest adding extra liquid when substituting 100% KIng Arthur white whole wheat for AP in a recipe. I've found that Trader Joe's brand doesn't need extra liquid.
I've actually made all my favorite muffin recipes healthier by swapping out white whole wheat for AP, using coconut oil in place of cooking oil and limiting the added sweetener to 1/2 cup or less per 12 muffins. I know have muffins for all seasons. Can't wait to try this recipe when raspberries are in season!
Connie says
Thanks, was just wondering about using white whole wheat instead. I use TJ white whole wheat and King Arthur, but TJ is cheaper and more convenient to get. I will look for the liquid use as you mention between the two,as I have wondered the difference between the two, thanks for the info.
Kristin says
For what it is worth I now mostly use WHOLE spelt flour (Bob's Red Mill is cheapest) for muffins at home. Spelt has lower gluten then whole wheat, and though not a gluten free household, I watch our intake. Muffins still come out fluffy, no extra liquid needed. I still use TJ's white wheat for muffins I take to school as BRM flours are not made in a nut free facility.
Nichole says
I made her applesauce and carrot muffins with only whole wheat and they were moist and delicious. Not rocks ;)
Caitlin says
I went to great harvest the other day and asked if their honey whole wheat had only whole wheat flour, because whenever I cook with only whole wheat, it turns out too dense. They said they add in some white flour or else it would be like a rock. I am really curious about this now since I notice you only use whole wheat in all I your recipes.
Lisa says
Which location? On the website where I go they post the ingredients and it does not include white flour. I only use 100% whole-wheat in my recipes. Unless it's cookies or some kind of treat!
Caitlin says
In VA. I saw that on the website too. Very odd!
Jennie R. says
Do I need to use frozen raspberries? I have fresh not frozen. How will it work with honey instead of maple syrup?
Lisa says
Honey will work just fine - I have not tried fresh raspberries in place, but I think it would work.
Sil says
The only difference is that fresh raspberries will "bleed" so for a nicer looking muffin better to use frozen. I'm currently waiting for my fresh berries to freeze while I'm doing something else in the house.
Dana K says
Sounds wonderful! Think you can sub butter with coconut oil and honey for maple syrup? I am new at baking; )
Lisa says
Yes, I think those subs would work just fine - 1:1 ratio. Let us know how it turns out!
Zamara says
This recipe sounds delicious!! Can't wait to try it. Thanks!
Andra says
Do you mix in the raspberries without thawing them? Is that so they are not oozing too much liquid? Also, would fresh work better?
Lisa says
I just used frozen because it's cheaper and easier - that's the only reason.
Carole says
I just made them with fresh raspberries and they turned out fantastic!
Elisa says
Do you put actual frozen strawberries in or do you defrost them first? So excited to try these!
Lisa says
Well, it's raspberries :) but yes - frozen!
Elisa says
Ha!! I have brain melt from dealing with a feisty 3 yr old. Thanks!!! going to make these right now :)
Isra says
Thanks for the recipe! Can we use honey instead of the maple syrup? Does maple syrup give it a certain taste that honey wouldnt?
Lisa says
Isra - Yes, it would slightly change the flavor, but that substitute would work just fine.
Brenda says
We love the Lunchbox Love Cards. Apparently, they are a big hit around the lunch table and get passed around quite a bit. I even had a teacher ask where she could get them for her son's lunchbox. To make them last longer for multiple uses, I use name badge holders (can be purchased in the office supply section). Each morning I just slide the cards in one of plastic sleeves before putting in the lunchbox. The cards have survived several spills and sticky fingers. We've used our many times over!
Lisa says
What a great idea to protect them! And same with my kids - they pass them around the lunch table to share. :)
Nicole says
Can you swap out the Whole Wheat flour for gluten free flour?
Lisa says
Nicole - Since we don't have any allergies or sensitivities I never cook with gluten-free flour so unfortunately cannot give you advice on that!
Jaime says
Nicole - one of the Baking Specialists at King Arthur Flour blogs for them about baking gluten free. Here is a link to a post that talks about converting recipes to gluten free. Hope it helps. http://www.kingarthurflour.com/blog/2013/07/26/the-gluten-free-conversion-conundrum/
Ann says
Do you use a specific kind/type of whole-wheat flour? There seems to be several options when I look at the store. These sound wonderful and can't wait to try them.
Lisa says
I recipe test with King Arthur flour.