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.
↓ Jump to Recipe
Whole-Wheat Lemon Raspberry Muffins from 100 Days of #RealFood

Want to Save this Recipe?

Enter your email below & we’ll send it straight to your inbox. Plus you’ll get great new recipes from us every week!

Save Recipe

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!

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.

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

Posts may contain affiliate links. If you purchase a product through an affiliate link, your cost will be the same but 100 Days of Real Food will automatically receive a small commission. Your support is greatly appreciated and helps us spread our message!

About The Author

376 thoughts on “Whole Wheat Lemon Raspberry Muffins”

Leave a Comment

Your email address will not be published. Required fields are marked *

Recipe Rating




  1. I have your Healthy Pumpkin Muffins in the oven right now – I make these all the time! Have you tried the Lemon Raspberry Muffins with spelt flour? I love that it gives the pumpkin muffins such a soft light texture – think it’s worth a try?

    1. 100 Days Admin

      Hi! We haven’t, but I think they would be worth trying out. Let us know if you give them a try. – Nicole

      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

  2. 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!

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

  4. 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. :-)