Healthy Cherry Muffins with Dark Chocolate Chunks

Healthy Cherry Muffins made with fresh cherries and dark chocolate chunks! This muffin recipe is easy to make and uses good-for-you ingredients like yoghurt, oatmeal, and wholegrain rye flour. It’s a cherry muffin the whole family will love!

a tray of cherry muffins on a grey background with fresh cherries scattered around

My favourite thing to do with cherries is eat them sun-warmed straight from the colander, separating the stem from fruit with my teeth and spitting the pit in an arc as I munch on the juicy flesh and my lips stain purple.

My second favourite thing to do with cherries is make these Healthy Cherry Muffins, which brings me to the business at hand. Let’s make some muffins!

Folks, it’s cherry time.

a white colander full of cherries

What’s in Healthy Cherry Muffins?

Here’s what you’ll need to get started:

  • Some leftover cooked oatmeal –> Yup, we’re using *cooked* oatmeal in these muffins to bump up the moisture. If you don’t have leftovers, you can make a super quick super small batch of oatmeal while you’re getting the other ingredients ready.
  • Wholegrain rye flour –> I love the grassy flavour of rye together with cherries and chocolate.
  • Bananas –> For moisture and sweetness.
  • Yoghurt –> For moisture and tang.
  • Butter –> Because we’re worth it.
  • Light brown sugar –> Don’t mind if I do.
  • A li’l bit of maple syrup –> Just a smidge.
  • An egg –> To hold everything together.
  • Fresh ripe cherries! –> Can’t really make cherry muffins without cherries, now can we?
  • Dark chocolate! –>Yes! Treat yo-self!

chocolate, brown sugar, cherries, butter, oatmeal, yoghurt, banana, egg, and flour on a grey background

How do I pit cherries?

Don’t let pitting the cherries scare you off from making these Healthy Cherry Muffins! There’s a cherry pitting hack that’s a total game changer – no fancy cherry pitting device required.

All you need is a sturdy straw – not a flimsy plastic one, but if you have a hard plastic, metal, or glass reusable straw, that’ll do the trick.

Here’s what you do:

  1. Hold a cherry in one hand and remove the stem.
  2. Place the straw into the groove where the stem was.
  3. With a firm but loving hold on your cherry, push the straw into the groove and out the other side.
  4. Pop! Your pit will just come on out.
  5. Place your pitted cherry in a bowl, and repeat steps 1-4 until you’ve got enough for this recipe.

cherries being pitted with a straw

Honestly, these muffins are a cinch to make! Once you get past the business of pitting the cherries – which I promise will take you all of three minutes – it’s just a matter of stirring everything together.

I’m a one-bowl operator when it comes to muffin making, so I do all the wet stuff, then add the dry stuff on top without sifting or premixing because I’m a rebel like that, and then after the base is mixed together the mix-ins go in last.

muffin batter with chopped chocolate and cherries being stirred in

Have you come across those dire warnings about not over-mixing your muffins? When I did my undergrad in nutrition I took a food science course where we did a muffin mixing lab. We made a batch of plain muffins and in the twelve muffin tins each muffin had been mixed a different number of times ranging from under-mixed to over mixed.

There is, indeed, a sweet spot in the just-barely-mixed area where you get the perfect crumb. Under mixed the muffins don’t hold together well, and over-mixed they become tougher and get big pockets of air.

But you know what? Even the over-mixed ones are still tasty AF so don’t sweat it.

muffin batter spooned into parchment lined muffin cups

Tips for making Healthy Cherry Muffins:

  • Do I really need to start with cooked oatmeal? Yes, please do. The recipe has been developed with a particular amount of moisture for a reason, and if you use dry oats instead it’ll mess things up.
  • I don’t have rye flour on hand. Do I need to buy a bag just for this recipe? If you happen to come across a small bag or you think you’ll use it in other recipes, then go for it. But you can certainly sub in another whole-grain flour. I’d choose spelt flour or whole wheat flour as substitutes.
  • Cherries aren’t in season, can I use a different kind of fruit? Totes, friends. Blueberries, raspberries, and blackberries would all be fab here.
  • Can I use frozen cherries? Sure thing! Just toss ’em in frozen and they’ll be just fine. Related: How to freeze cherries.
  • Can I omit the chocolate? If you must, but I heartily encourage you to keep it in.
  • Can these muffins be frozen? You bet your booty they can! Just cool them and then toss into a freezer bag.
  • Can I make a double batch? Yes you can! Just change the number of muffins in the recipe card below, and it’ll automatically change the quantities for you.

cherry muffins cooling on a wire rack

Hey Nutrition Lady, what’s the deal with cherries?

I thought you’d never ask!

Cherries are rich in antioxidants: they’re rich in beta carotene, vitamin C, anthocyanins and quercetin, which are thought to work together to fight cancer.

When it comes to cherries, the riper the better: as cherries ripen (and darken), they produce more antioxidants. The antioxidant quercetin, which is also abundant in cherries, may help regulate blood pressure.

Cherries are also loaded with potassium, which works to reduce blood pressure naturally. Potassium helps to balance fluids in our bodies, working to offset the effects of sodium. One cup of ripe cherries packs roughly the same amount of potassium as a small banana!

Another benefit of cherries is their dietary fiber content. With 3 grams of fiber per cup, cherries provide 13 percent of the recommended daily amount. Fiber helps to regulate blood sugar, promotes healthy digestion, and prevents constipation.

overhead photo of a tin of cherry muffins with one muffin removed and broken in half, and some cherries scattered around

Other healthy muffins you might enjoy:

Whole Wheat Muffins with Cinnamon Roasted Apples
No Sugar Banana Bran Muffins
Carrot Pineapple Muffins
Healthy Pumpkin Muffins
Savory Cottage Cheese Muffins


a tray of cherry muffins on a grey background with a couple of muffins removed from the tin and fresh cherries scattered around
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5 from 6 votes

Healthy Cherry Muffins

Healthy Cherry Muffins made with fresh cherries and dark chocolate chunks! This muffin recipe is easy to make and uses good-for-you ingredients like yoghurt, oatmeal, and wholegrain rye flour. It's a cherry muffin the whole family will love!
Course muffins
Cuisine American
Keyword cherries, chocolate, muffins
Prep Time 15 minutes
Cook Time 35 minutes
Total Time 50 minutes
Servings 12 muffins
Calories 220kcal
Author Katie Trant


  • 1/4 cup room temperature butter
  • 1/4 cup light brown muscovado sugar
  • 1 large egg
  • 2 large bananas mashed
  • 3/4 cup cooked oatmeal cooked and cooled
  • 1/2 cup plain yoghurt
  • 2 Tbsp maple syrup
  • 1 cup wholegrain rye flour
  • 1 cup all purpose flour
  • 1 1/2 tsp baking powder
  • 1/2 tsp baking soda
  • 1/2 tsp fine-grain salt
  • 1 cup pitted and halved cherries measure after cutting in half
  • 3 ounces chopped dark chocolate


  • Preheat your oven to 350°F / 180°C. Line a 12-cup muffin-tin with parchment paper or muffin cases. 
  •  In a large bowl combine butter and sugar until fluffy, using an electric mixer.
  • Add the egg, mixing until well incorporated, and then add mashed bananas, oatmeal, yoghurt, and maple syrup. Mix well. 
  • Add the flours, baking powder, baking soda, and salt, folding the mixture together until just combined.
  • Add the cherries and chocolate as well, folding through the muffin batter. 
  • Spoon mixture into prepared muffin tins. 
  • Bake for 35 - 40 min, rotating the pan once half way through. The muffins are done when golden on top, and when a knife inserted into the middle has only a few moist crumbs clinging to it.
  • Cool the muffins on a wire rack for at least 5 minutes before you dig in. 


Nutrition values are an estimate only.


Calories: 220kcal | Carbohydrates: 33g | Protein: 4g | Fat: 8g | Saturated Fat: 4g | Cholesterol: 27mg | Sodium: 198mg | Potassium: 308mg | Fiber: 3g | Sugar: 13g | Vitamin A: 175IU | Vitamin C: 2.8mg | Calcium: 63mg | Iron: 1.9mg

This recipe was originally published July 24, 2011. It was retested, rephotographed, and updated on July 10, 2018. Last updated June 23, 2020. 



  1. Caroline says

    So I made a vegan version of these and they are delicious but also taste nutritious which is a winning combo for me! Instead of butter and yoghurt I used dairy free alternatives. Instead of egg I used a cheat mixture of 1 tsp baking soda and 1 tea spoon of malt vinegar. The texture of the muffins turned out perfect! I cooked for a little less time than the recipe suggested, I think about 32 minutes. They smelt so good I checked on them and they were ready! Also I have a fan oven so I think the temperature was a little hotter too. Thank you!

  2. Katie says

    My twin 2 year-olds are devouring these (half of me is delighted and half of me would rather keep them to myself…).
    Thank you for all of the notes on substitutions. In the end we were out of rye flour, were low on maple syrup and had only one banana, extremely ripe… Whole wheat flour, 50/50 maple syrup and molasses, and 50/50 banana and apple sauce substitutions all worked really well.

    • Katie Trant says

      I haven’t tried making these muffins vegan so can’t say for sure how they’d turn out. If I had to guess, I’d suggest subbing a vegan yogurt or silken tofu for the yogurt, and your favourite egg replacer for the eggs. But like I said, this is just a guess!

  3. alice k mynett says

    I wish your ratings had a 6th star, as that’s what these would warrant. Served them for brunch and for a moment all I could hear was “Mmmmm”. So delicious! I didn’t have a straw in the house, but I did find my turkey baster, so I used the end of that … a firm push and the pits almost hit the opposite wall. Worked like a dream. (I think the end of my funnel would have worked as well.) This has been a fabulous season for cherries in Vancouver, so I have stocked my freezer with pitted cherries to enjoy these muffins in the winter. Thank you!

  4. MNAsh says

    I cant wait to try these! Love the flavour combo.
    Perhaps in lieu of yoghurt you could use applesauce?
    Thanks Katie!

    • Katie Trant says

      Hey Hanna, good question. I haven’t tried making this recipe without the yoghurt, so I can’t say for sure how it would turn out with something different, but I’d be inclined to try adding an extra banana instead, or using some coconut yoghurt in place of regular. If you try this, please let us know what you do and how it turns out!

  5. Tara says

    Can’t wait to try this one:) If I do not have rye flour handy and am using whole wheat would the cooking time still be the same?

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