I have some lemon-kissed Raspberry Muffins love for you! These dome-topped, berry-studded, ultra-fluffy muffins are sweet, whole wheat, and worthy of that pricey, precious carton of ruby red raspberries you’ve been coveting.

Healthy Raspberry Muffins. Moist and DELICIOUS! Easy homemade recipe for lemon raspberry muffins that are whole wheat, naturally sweetened, and made with Greek yogurt. Use fresh or frozen raspberries or swap in any of your other favorite summer fruits. Great for healthy breakfasts and healthy snacks!

Whether you need a pink-studded Valentine’s treat, a healthy breakfast or snack you can take on the go, or a kid-approved baking project, these moist, healthy Raspberry Muffins are a bright berry burst of sunshine you’ll love waking up to every morning they grace your kitchen.

Which, if your house shares our warm sentiments towards Raspberry Muffins, will turn out to be fewer mornings than you please. Might I suggest a double batch?

Healthy Lemon Raspberry Muffins. Moist, fluffy, and absolutely delicious! Great for healthy breakfasts and snacks.

About This Healthy Raspberry Muffins Recipe

Like nearly all of the healthy muffin recipes you’ll find on my site, these Raspberry Muffins are whole grain, naturally sweetened, and employ a few sneaky tricks to make them super moist without the need for excess fat.

  • For an extra nutritional boost, I added flaxseed meal to the raspberry muffin batter instead of an egg. You won’t taste it, but you’ll love taking an extra bite knowing that you’re enjoying its omega-3 benefits.
  • I also took inspiration from recipes for sour cream raspberry muffins but swapped Greek yogurt instead.

You’ll find delicate, sweet berries in every bite, a soft-springy crumb, and a refreshing, perky touch of lemon.

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

Even though I know firsthand how easy these lemon Raspberry Muffins are to make, every morning that I sat down with one (warmed up and smeared lightly with nut butter, thank you very much), I felt like a queen.

Healthy Raspberry Muffins with Lemon, Greek yogurt, and whole wheat flour. Easy, moist, and delicious!

While I’ve played around with adding a variety of different fruits (and even veggies!) to my muffins—Healthy Blueberry MuffinsBanana Oatmeal MuffinsChocolate Zucchini Muffins(with avocado), and Vegan Pumpkin Muffins—this was my first foray with raspberries.

Cupid must be doing his job, because I am smitten!

Raspberries are more delicate than other fruits, so they will break apart in the batter somewhat as you gently stir them in; the way I see it, that just means more bits of raspberry in each bite.

Raspberry Muffins–Recipe Adaptations

  • For 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.
  • For 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.
  • For 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.

Using Frozen Raspberries to Make Muffins

  • In the summer, these muffins are sublime with peak-season fresh raspberries. You can spring for fresh at other times of year if you like, but it’s not 100% necessary because…
  • At every other time of year, these Raspberry Muffins are fabulous with frozen raspberries too! I have added notes for how to use frozen berries to make muffins in the recipe below.

Recommended Tools to Make Healthy Raspberry Muffins

Healthy Raspberry Muffins. Moist and DELICIOUS! Easy homemade recipe for lemon raspberry muffins that are whole wheat, naturally sweetened, and made with Greek yogurt. Use fresh or frozen raspberries or swap in any of your other favorite summer fruits. Great for healthy breakfasts and healthy snacks!

Raspberry Muffins

5 from 10 votes
Healthy raspberry muffins with lemon. Moist, loaded with raspberries, and absolutely delicious! Use fresh or frozen berries to enjoy the recipe year round.

Prep: 25 mins
Cook: 20 mins
Total: 45 mins

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 (I love a big scoop like this one). 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 to the wire rack to cool completely (do not leave the muffins in the pan, as they will steam and become tough). Enjoy!


Serving: 1muffinCalories: 172kcalCarbohydrates: 23gProtein: 6gFat: 6gSaturated Fat: 3gCholesterol: 42mgSodium: 126mgFiber: 5gSugar: 9g

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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 wellplated.com 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!

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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: https://www.wellplated.com/healthy-blueberry-muffins/. 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. I’m definitely a eat-fruit-by-the-handful kind of person too! Usually just reaching in and grabbing some before dinner while I cook. But I will definitely be trying these out. I love the use of flaxseed meal!

  3. 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!

  4. 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

  5. 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!

  6. 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!

  7. 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

  8. These sound so delicious. I love making different kinds of muffins. Being able to use frozen raspberries is nice when fresh are not in season.

  9. 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

  10. Muffins are my all time favorite and love eating them anytime. I have not tried muffins with raspberry so I am gonna make them on this weekend and let you know my experience later. Hoping I make them as tasty as you make. Thanks5 stars

  11. 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!

  12. 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!

  13. 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!