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These dome-topped, berry-studded, ultra-fluffy Raspberry Muffins are sweet, whole wheat, and worthy of that pricey, precious carton of ruby red raspberries you’ve been coveting.

healthy raspberry muffins whole wheat on a plate with lemon and fresh berries

Whether you need a healthy breakfast, an on-the-go snack, or a kid-approved baking project, you’ll love waking up to these moist raspberry muffins every morning (or these Cranberry Orange Muffins).

And, if your house shares our warm sentiments towards raspberry muffins, these are not likely to last as many mornings as you intended.

Might I suggest a double batch?

Whole wheat raspberry muffin batter with lemon in a bowl with fresh raspberries

5 Star Review

“This is a wonderful healthy muffin recipe!”

— Audrey —

Eating a homemade, healthy muffin for breakfast always makes me feel special (thank you, Carrot Cake Muffins).

Even though I know firsthand how easy these lemon Raspberry Muffins are to make, I felt like a queen every morning that I sat down with one.

Like many of my muffin recipes, these raspberry muffins are whole grain and employ a few sneaky tricks to make them super moist and healthy:

  • I added some flaxseed meal to the raspberry muffin batter for an extra nutritional boost. You won’t taste it, but you’ll love taking an extra bite knowing that you’re enjoying some added omega-3 benefits.
  • I also took inspiration from raspberry muffin recipes with sour cream. I added a few dollops of Greek yogurt to this healthy muffin recipe (like in these Yogurt Muffins).
  • The goodness of honey or maple syrup naturally sweetens this muffin recipe (and these Banana Bran Muffins) just enough to keep the muffins tender, moist, and subtlety sweet.
Healthy raspberry muffins with lemon are easy, moist, and naturally sweetened with honey or maple syrup

How to Make Raspberry Muffins

While I’ve played around with adding various fruits (and even veggies!) to muffins—Banana Oatmeal MuffinsChocolate Zucchini Muffins, and Vegan Pumpkin Muffins—this was my first foray into homemade muffins with raspberries.

Using Frozen Raspberries to Make Muffins

In the summer, these muffins are sublime with peak-season fresh raspberries. While you can spring for fresh at other times of the year, it’s not 100% necessary.

That’s because you can enjoy these raspberry muffins with frozen raspberries too! In the recipe box below, I have added notes on how to use frozen berries to make muffins.

The Ingredients

  • Raspberries. More delicate than other fruits, these juicy berries break apart in the batter as they’re gently stirred in. The way I see it, that just means more bits of raspberry in each bite.
  • White Whole Wheat Flour. Boost the nutritional content of this healthy muffin recipe with extra fiber and iron without sacrificing texture.

Substitution Tip

If you do not keep white whole wheat flour on hand, you can swap it for an equal amount of all purpose flour or a blend of half regular wheat flour and half all-purpose.

  • Flaxseed Meal. For a hidden kick of added fiber and omega-3 goodness to these whole wheat raspberry muffins. (I also like to sneak a scoop into these Healthy Banana Chocolate Chip Muffins.)
  • Baking Powder + Baking Soda. For a double punch of leavening action to give these muffins a supreme rise and domed top.
  • Butter. For flavor and just enough necessary fat to tenderize the muffins and keep them moist.

Substitution Tip

I have not made these raspberry muffins without butter before. However, readers have reported successfully making these raspberry muffins with coconut oil and vegetable oil.

  • Honey. My preferred natural sweetener for these muffins (and these Coffee Cake Muffins). It pairs perfectly with the tart raspberries and white whole wheat flour.

Substitution Tip

If you don’t have honey, maple syrup is an equally divine choice for sweetener in these easy raspberry muffins.

  • Eggs. Provide structure and tenderness.
  • Greek Yogurt. My swap for sour cream that adds softness and tang to these moist raspberry muffins. (I also add Greek yogurt to my favorite Healthy Banana Muffins recipe.)
  • Vanilla. Complements the raspberries and balances all the flavors.
  • Lemon. For a little unexpected brightness, I add fresh lemon juice and zest to these fresh raspberry muffins. (These Orange Muffins with Poppy Seeds are also bursting with bright citrus flavor.)
  • Turbinado Sugar. A sprinkle on top makes them look (and taste) like they came straight out of a professional bakery case.

The Directions

  1. Whisk together the dry ingredients. In a separate bowl, beat wet ingredients together.
  2. Add the dry ingredients to the wet ingredients, mixing by hand until just combined.
  3. Gently fold in the raspberries.
  4. Scoop the batter into a greased or lined standard-size muffin pan.


For a maximum crunchy top, sprinkle each muffin with a full teaspoon of turbinado sugar (trust me!) or omit for a less-sweet muffin.

  1. Bake raspberry muffins at 375 degrees F for 20 to 24 minutes until a toothpick inserted in the center comes out clean. ENJOY!

Recipe Adaptations

  • Vegan Lemon Raspberry Muffins. I haven’t tried this yet, but I think you could safely swap flax eggs for the regular eggs, coconut oil for the butter, and a non-dairy, coconut-based yogurt for the Greek yogurt.
  • Raspberry Streusel Muffins. Make the recipe as directed, omitting the turbinado sugar sprinkled on top. Instead, top the muffins with the streusel recipe called for in these Healthy Oatmeal Muffins.
  • Healthy Raspberry Zucchini Muffins. Start with this recipe for Healthy Zucchini Muffins, swapping raspberries for the chocolate chips. You can also add lemon zest if you like.
  • For Raspberry Muffins with Frozen Raspberries: Prepare the recipe as directed, swapping the fresh raspberries for an equal amount of frozen berries. No need to thaw!

Storage Tips

  • To Store. Leftover raspberry muffins will keep well in an airtight container at room temperature for 2 to 3 days.
  • To Freeze. To freeze raspberry muffins, store them in a single layer on a baking sheet and freeze until solid. Transfer the frozen muffins to an airtight freezer-safe storage container or ziptop bag for up to 3 months. Thaw and enjoy as desired.

Storage Tips

Check out my Healthy Muffins – Easy Recipes, Storage Tips, and More post for more great muffin storage tips.

What to Serve with Raspberry Muffins

Recommended Tools to Make this Recipe

Fresh or frozen, muffins with raspberries are a true treat!

Frequently Asked Questions

Can I Substitute Raspberries for Blueberries in Muffins?

Sure! In most muffin recipes (including these Healthy Blueberry Muffins), you can swap fresh or frozen raspberries for blueberries (and vice versa) with success.

Can I Make Raspberry Muffins with Buttermilk?

I have not experimented with adding buttermilk to this recipe before. If you’re looking for a fantastic raspberry muffin recipe with buttermilk, I suggest using this Buttermilk Blueberry Muffins recipe as a base and swapping for raspberries.

Can I Make Lemon Raspberry Muffins Without Yogurt?

If you want to omit the Greek yogurt, you could try swapping it for sour cream.

Raspberry Muffins

4.93 from 14 votes
The BEST raspberry muffin recipe with lemon. Moist and easy, these healthy raspberry muffins with whole wheat flour are naturally sweetened.

Prep: 25 minutes
Cook: 20 minutes
Total: 45 minutes

Servings: 12 muffins


  • 2 cups white whole wheat flour
  • 1/4 cup  ground flaxseed meal
  • 1 1/2 teaspoons baking powder
  • 1/2 teaspoon baking soda
  • 1/2 teaspoon kosher salt
  • 1/4 cup unsalted butter at room temperature
  • 1/3 cup honey or pure maple syrup
  • 2 large eggs at room temperature
  • 1/2 cup nonfat plain Greek yogurt at room temperature
  • 2 teaspoons pure vanilla extract
  • Zest of 2 small lemons about 1 1/2 teaspoons
  • 1/4 cup lemon juice from the same 2 small lemons
  • 1 1/2 cups raspberries fresh or frozen (about 1 1/2 6-ounce containers); if using frozen, do not thaw first
  • 3 tablespoons turbinado sugar in the raw sugar, for topping (optional)


  • Preheat the oven to 375 degrees F. Lightly coat a standard 12-cup muffin tin with nonstick spray or line with paper liners.
  • In a medium bowl, whisk together the white whole wheat flour, flaxseed, baking powder, baking soda, and salt.
  • In a large separate bowl, beat the butter and honey until creamy and combined. Scrape the bottom and sides of the bowl, then add the eggs one at a time, beating well after each addition. Add the Greek yogurt, vanilla, lemon zest, and lemon juice. The batter may look curdled.
  • Add the dry ingredients to the wet ingredients. By hand with a wooden spatula or spoon, stir in the dry ingredients, just until the flour disappears. The batter will be very thick.
  • Very gently fold in the raspberries.
  • Scoop the batter into the prepared muffin cups, using a heaping 1/4 cup for each. For a maximum crunchy top, sprinkle each muffin with a full teaspoon of turbinado sugar (trust me!) or omit for a less-sweet muffin.
  • Bake the muffins for 20 to 24 minutes, until a toothpick inserted in the center comes out clean.
  • Remove the from the oven and place on a wire rack to cool in the pan for 5 minutes. After 5 minutes, remove the muffins from the pan and transfer them to the wire rack to cool completely. Enjoy!



  • TO STORE: Leftover raspberry muffins will keep well in an airtight container at room temperature for 2 to 3 days.
  • TO FREEZE: To freeze raspberry muffins, store them in a single layer on a baking sheet and freeze until solid. Transfer the frozen muffins to an airtight freezer-safe storage container or ziptop bag for up to 3 months. Thaw and enjoy as desired.


Serving: 1muffinCalories: 196kcalCarbohydrates: 29gProtein: 6gFat: 7gSaturated Fat: 3gPolyunsaturated Fat: 2gMonounsaturated Fat: 2gTrans Fat: 0.2gCholesterol: 42mgPotassium: 172mgFiber: 4gSugar: 12gVitamin A: 169IUVitamin C: 6mgCalcium: 68mgIron: 1mg

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Erin Clarke

Hi, I'm Erin Clarke, and I'm fearlessly dedicated to making healthy food that's affordable, easy-to-make, and best of all DELISH. I'm the author and recipe developer here at and of The Well Plated Cookbook. I adore both sweets and veggies, and I am on a mission to save you time and dishes. WELCOME!

Learn more about Erin

4.93 from 14 votes (6 ratings without comment)

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  1. Erin, these sound wonderful! My husband can’t have flaxseed so what would be a suitable substitute? I make muffins all the time and follow your advice about their storage – paper towel lined container and a piece on top. Keeps the “soggys” away…not a very technical term but it does get the point across, huh?

    1. Chris, I’d actually recommend making these healthy blueberry muffins, but add raspberries instead of the blueberries, plus a teaspoon or two of lemon zest: That way the recipe will come out perfectly! Removing the flax, unfortunately, I don’t think will work super well, as it behaves uniquely. I’m so happy the storage tips have been helpful too!

  2. Can I substitute agave for the honey/maple syrup? I just found your blog the other day, I’ve already made a couple of the recipes, and they are wonderful. Thank you!

    1. SO HAPPY you are loving the recipes sor far Aislinn! And yes, you can use the same amount of light agave nectar. I hope you love them!

  3. These are the best!  Made them for a friend, whose favorite summer fruit is the raspberry. She ate one in the car on the way home, unable to resist them, then finished the rest without sharing. (Half a batch). Thanks for this excellent way to make muffins super delish!  5 stars

  4. Given my husband has Celiac, I converted these to GF. I had accidentally bought the incorrect GF all purpose flour by Bob’s Red Mill that requires the addition of xantham gum. So the texture of our muffins is certainly different, but it is an amazing recipe! I love that they’re not overly sweet and can be eaten as is or sprinkled with sugar, drizzled with nut butter, or broken up over a bowl of Greek yogurt. I definitely recommend them!5 stars

    1. Kori YAY!!! Thanks so much for trying the recipe and taking time to leave this fabulous review and your tweaks too! I’m glad they still worked out :)

    1. Hi Mehwish, you could substitute coconut oil, but the muffins may be a little more dense, and they won’t have the same buttery taste. (If you want to try to keep the buttery taste, I’d recommend using a vegan butter substitute.) I hope you enjoy the muffins!

  5. Dying to try this recipe – can i substitute blueberries instead? If so, frozen or fresh and would it be the same amount? Thank you so much!

    1. Hi A, I haven’t made the muffins without, but they will have a different flavor. You could give it a try, but I would recommend subbing another liquid for the 1/4 cup lemon juice.

    1. Hi Gavi! I haven’t tried this yet, but I think you could safely swap flax eggs for the regular eggs. I hope you enjoy the muffins!

  6. We made the raspberry muffins two nights ago and they were delicious. I can’t wait to catch up with all your ‘Recipe’!!5 stars

  7. Erin, you precisely expressed how I covet that expensive jewel of the raspberry! My husband laughs at how much I will spend for them and the amount of flaxseed meal that I use. These muffins are amazing, thank you for the recipe.5 stars

  8. Oh Erin, these are some delicious, easy to make, healthy muffins!  Your ingredients are so well thought out, the measurements, directions, and tips are spot on and your videos are simply wonderful. I used a 10 oz bag of frozen raspberries which worked well even though I dumped in the whole bag which led to just a slight over-the-top moistness, but tons of raspberrylishousness!  Thank you!5 stars

    1. You MADE my day! I’m so happy to hear that this was a hit, Geni! Thank you for taking the time to share this kind review!

  9. This recipe was delicious. We had them for my little daughter’s birthday, it was lovely to have a relatively healthy option for us to enjoy with a candle in!5 stars

    1. I’m so happy that you enjoyed the muffins, Frances! Thank you for sharing this kind review!

  10. This is a wonderful healthy muffin recipe! My daughter and I love muffins at all times of the day. These are so yummy! Can’t wait to try more of your healthy muffin recipes! Thank you for sharing this. ?5 stars

    1. Hi Najeeha! Since I’ve only tested the recipe as written, it would be a complete experiment. If you decide to play around with it, I’d love to hear how it goes!

  11. Used einkorn flour instead of WW and added some dark chocolate bar. So yummy! I upped the raspberries to 2.5 cups because we picked so many. They still turned out perfectly! Will definitely make these beauties again.5 stars