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






Noah A says
I just made these muffins for the first time, and they were phenomenal! My spouse and kids all loved them too! Thanks for the recipe Lisa, and for all of the fantastic advice with the healthy eating!
Tammy says
I have a real aversion to maple syrup. Can you tell me what would be a good substitution? They look so yummy!
Rebecca says
You could use Agave!
Assistant to 100 Days (Amy) says
Hello Tammy. You could also try honey. ~Amy
Emily Jane says
So yum! I love raspberry.
Here is another one of my latest breakfast cravings:
http://www.eastofvanwinkle.com/2014/04/whole-wheat-pumpkin-pancakes.html
Thanks so much for such a great resource for real food recipes!
Kim says
apparently I am the only one who had difficulty with this recipe. (I am not new to cooking unprocessed and am considered a pretty good cook by my friends)... I have made ALL of Lisa's muffin recipes, and loved them all...but with this one, the butter was too hard and clumped together. I think maybe my Maple syrup (grade B, for baking?) and milk was too cool, and made the room temperature butter coagulate...I have also had trouble using her recipes with coconut oil...same reason- perhaps being that I am in Montana, much higher elevation and not nearly as warm, these techniques do not work on our kitchen. so, beware- your ingredients have to all be room temp!! I still struggle with the coconut oil...even though I refuse to use canola or vegetable....
and PS- Bob's Red Mill makes a white whole wheat flour that is ORGANIC, so I have switched from King Arthur which I cannot find in organic....
Azalea Bell says
My butter did the same thing. I guess the refrigerated ingredients need to be room temp.
Kristin says
I haven't tried this recipe yet so I cannot attest to it but when I use coconut oil in a recipe I temper it in and it helps to keep it from solidifying back up. So for example, when I make pancake batter, I slowly drizzle the melted coconut oil into the bowl last as I whisk the ingredients together. This works really well. Otherwise I end up with big chunks of coconut oil in my batter.
Ann says
The recipe calls for softened butter which means room temp. With baking it's usually best to have everything at room temperature (unless otherwise specified). I'm not sure of the science behind it, but it really does make everything come out better.
Loved this recipe!
Rachel says
I had the same problem with the butter, which I even left on the counter overnight to soften. I also left my maple syrup and my milk on the counter for a hour, and my butter still clumped together. I heated the liquid ingredients on the stove until just blended, and my muffins still turned out beautifully. I don't know what other trick besides warming up the butter to try?
Amy says
These were so delicious!!
Heidi says
Lisa, these are amazing! One out of my 3 boys is a really particular eater -- the kind who will find one zest of the lemon zest in a muffin and reject the whole thing. Well, guess what? He devoured these!! Thanks so much for the great recipe. The flavors are fantastic, and you wouldn't believe you are eating a 100% whole wheat muffin.
Gale says
Definitely a winner in our house. My sons are 3 and 1, and both gobbled these up!
Mandy Cheshire says
I just made these, and the only thing I did different was use a frozen berry mix, as that is what I had on hand. They turned out PERFECT! Wonderful-tasting muffin and SO soft!They also were easy and quick to make. I can't wait to serve these to my family for breakfast.
Meagan says
Just made these this morning! Added the juice of a whole lemon and used fresh raspberries instead of frozen. They were great!
Sev says
Just made these and they are great, not too sweet!
Carolyn says
I really struggled making these muffins. I had nice soft butter, but when I added the other ingredients (straight from the fridge) it lumped all that butter right back up! I worked through it and the end result was just awesome. My picky, picky daughter loves them - is even taking them to school for a snack. She is only in 1/2 day kindergarten so she only gets a snack. She said, "Mom, I want to take something healthy". SCORE!
Carolyn says
Oh - and I used blueberries instead of raspberries - because that is what I had.
Rebecca says
I buy fresh frozen raspberries in bulk about once a year from a farm. I'm also just begining to cut out processed foods for myself...then later on the goal is my family.
I would like to try these using lemon essential oil...
Brooke says
Just made these and the Applesauce-Carrot muffins for the first time with my 4-year old and WOW!! I haven't tried the carrot yet, but we split a Lemon Raspberry, and I'm in love!! Can anyone help me out with the best way to store these? I'm new to baking with wheat flour, so I want to make sure they don't go bad before the family breakfast get-together on Saturday (which was the reason we baked 2 dozen) :). Thanks!!
Jessica says
I have these on my list for this weekend but with the carrot muffins and the pumpkin spelt ones I prefer to eat them same day or freeze immediately. Then I just take them out of the freezer either right before bed the night before (if we will have them for breakfast) or if for lunch I can usually take them out early morning. I think they freeze very well and I am not usually one to freeze many things.
Candice says
Just made these for the second time. Followed to the T the first time. They were so good my nine year old sugar-holic was eating them three at a time. The second time I sub'd 1/2 cup of the flour with flax meal and added blueberries. OMG I think I will be eating them three at a time. YUMMEE! Thnx
April says
These are so delicious!!! I wouldn't change a thing. Yes, they are a treat and we won't be eating them on a daily basis, but very tasty!
Chaylin says
I was wondering if anyone used coconut or almond flour with these instead of wheat??
Assistant to 100 Days (Amy) says
Hi Chaylin. We have not and you could not sub them 1:1. I think you would need to try a combo of flours but not sure what that would be. Let us know if you do. ~Amy
Courtney says
I used 3/4 c of cashew meal and 3/4 oat flour (GF) and 1/4 c of applesauce in place of half the butter-turned out great! also added a little lemon juice
Allison says
Has anyone tried to make these using some applesauce instead of butter, or reducing the amount of butter all together? An entire stick for 12 muffins make these seem like dessert. We are trying very hard to reduce the amount of animal protein we consume.
Jill says
You can substitute coconut oil for butter. Not an animal fat & healthy. You can usually sub about 1/4 - 1/2 of butter with apple sauce but not all of it.
Elisa says
Made these last week and they were amazing!!! We used honey, because thats what we had on hand and they were quite sweet. Also, totally messed up and added the WHOLE bag of frozen raspberries instead of just a cup and they were still great. Totally foolproof recipe.
Danielle says
Just made these and they are amazing! Didn't change a thing!!!
Kari Brown says
Great recipe:) I used blueberries in mine and they were fab!
Jenn says
Hello! I just made these muffins and I was worried when they came out looking kind of gray. Not very appetizing. However, I tasted one and they taste great. I looked back at the recipe here and noticed yours look a little gray too. Wonder what that is... Anyway, they taste great! Thanks for sharing the recipe!
Courtenay says
Another great recipe Lisa! After reading some of the comments I added some lemon juice along with the lemon zest (love our microplaner) and they are deeelicious, as you reported. We enjoy all your muffin recipes. They are a great for breakfast or lunch, since we don't do cereal here anymore, and when my kids tire of sandwiches.
Sarah says
I Have been waiting all week to make these for a Sunday morning treat. They are baking now. I'm pretty excited. They sound and smell delicious. I added a bit of a raw sugar streusel to the top, which I normally wouldn't do but it's our Sunday treat so what the heck! I am hoping they turn out ok. I just noticed I accidentally used a 2/3 measuring cup thinking it was a 1/2 measuring cup to measure out the flour. I thought they seamed a bit thick when mixing so I added the juice of my zested leamon to thin a bit. I'm going to be so sad if I messed them up. I have been so excited for them I can practly taste them all week. Fingers crossed!
Sarah says
Turned out great! A little crumbly from the extra flour, but DELICIOUS!
Sandmama says
Made these this morning. They work great with cranberries and orange (thought I had raspberries, but a munchkin ate them).
Perfect antidote to store-bought muffins.
Susan says
I made these yesterday afternoon in an 8x8 pan b/c I didn't have any cupcake papers. Baked for about 25 min to get totally done. Very good even though I folded in all the berries and looked down and realized I never put the darn egg in (I'm not a strong cook!) so I had to beat the batter with the berries in it which made the muffin cake a very strange color, but it tasted the same so it was all good. Great recipe. Thanks for posting.
Missy says
These are delicious. I added the juice from a whole lemon to make them more lemony.
Becky says
This was delicious. I made a few changes because I didn't have everything on hand. I used unsweetened applesauce in place of the butter (1:1) and spelt flour instead of whole wheat flour. I made this as a bread loaf since I did not have muffin liners on hand. I baked in a loaf pan for 50 minutes and my entire family has gobbled it up. Very happy how well this turned out with the changes and will make again soon! :)
Shannon says
I made these last night with my 4 year old. My parents are visiting and everyone LOVED them!
Nancy says
Great flavor and consistency! Definitely a keeper, but if you are expecting sweet, these are not! I will make again!!!
Katie says
Made these tonight and loved them! I used a "flax egg" since one son is allergic and they were still great. They weren't very lemony so I may add some juice as others suggested. I'm excited for the kids to try them tomorrow morning!
Maddy says
WOW! I just made these. I am new to the whole cutting out processed foods thing. I have had whole wheat flour in the cupboard for quite a while but I never knew what to do with it. These are amazing! Even my family who claims they don't like whole wheat loves these.
I did make a few alterations, based on what I had. I ran out of maple syrup so I substituted a little honey. I also used frozen blueberries instead of raspberries. They were equally delicious. Lastly, I added about four tablespoons of fresh lemon juice into the batter along with the zest. This have the muffins a nice lemon flavor. I never knew real food could taste so good!
And these recipes are sooo easy to make alterations to- love that! :D
For some reason it won't let me rate this recipe, but if I could, I would give this five stars. Thanks for an amazing recipe, Lisa. :)
Kelley says
Made these this morning with coconut oil instead of butter and used the zest of 1 lemon plus the juice. Wow these are so yummy and even my husband liked them! He is hard to please when food is made with healthy ingredients. Thanks for the recipe!
Jessica says
I just made these last night, the kids didnt love them. They arent huge fruit muffin people. BUT I however could sit down and eat an entire batch. I love the combination of lemon and strawberry/raspberry so much that i made a smoothie this morning for breakfast! mmm! Thanks so much!
Ashley Cox says
My family loves all your muffin recipes (particularly my 6-year-old son who would practically eat them for breakfast, lunch and dinner if I let him)! I made these yesterday and they are definitely a nice change from carrot//applesauce which we also love! My son gobbled it down and asked me to pack it in his snack every day! I typically sub 1/2 cup of the whole wheat flour with ground flax meal and coconut oil for the butter (with these on the first try I only subbed half of the amount of butter with coconut oil). They came out perfect! Please continue to post more great muffin recipes! I love keeping some in the freezer for quick breakfasts and snacks. Has been invaluable to have on hand for keeping us off of processed food!
Kristy David says
Just made these & they are so good! Love how a muffin recipe can be so delicious without any sugar :)
christina says
I love your website and all your recipes and what you stand for. Thank you for educating people on the importance of wholesome foods! My husband and son have to be on a gluten free diet. Do you have suggestions for gluten free alternatives to whole wheat?
Assistant to 100 Days (Amy) says
Hi Christina. This post might help: https://www.100daysofrealfood.com/2012/06/28/food-allergies/ and this website is a great source for gluten free recipes: http://deliciouslyorganic.net/. ~Amy
Rena says
I made this tonight but replaced the milk with almond milk and, by accident, forgot to add the frozen raspberries. They turned out great, even without the raspberries! My 6 year old ate 1 and says they are good! We'll see how he feels tomorrow! ;)
Lindsay says
Could you use regular all - purpose flour and if so, would the amount change?
Assistant to 100 Days (Amy) says
Hi Lindsay. We've not used white flour. This might help:http://www.kitchensavvy.com/journal/2005/01/substituting_wh.html?cid=92980014. ~Amy
Aprille Rollins says
I was wondering if you could use honey instead of maple syrup? Has anyone tried it that way?
Assistant to 100 Days (Amy) says
Hi April. We haven't tried but it should work. ~Amy
Kim Packard says
Made these this morning. Delicious! I'm going to try blueberries next time for fun.