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GET IT NOWMy Coffee Cake Muffins Taste Like A Bakery Treat, But Are Secretly Good For You

Say hello to your new favorite better-for-you bakery-style treat. Coffee cake is one of my favorite kinds of morning sweets, but I wanted something more portable. And that’s how these coffee cake muffins came about. Here’s why they turned out to be some of the best muffins I’ve ever made:
- Sweet, moist muffins with cinnamon ribbons, cream cheese filling, and streusel topping – This coffee cake muffin recipe has all the elements of your favorite coffee cake, just in muffin form! And that makes them feel like so much more than “just a muffin”.
- Simple, feel good ingredients – I make these with almond flour and no added sugar, so they’re naturally gluten-free. But what really surprised me is each one has over 9 grams of protein and almost 4 grams of fiber! And you’d never know from the taste.
- Easy and versatile – I equally love to meal prep these coffee cake muffins for easy weekday breakfasts and to make fresh ones for holiday mornings.
If you’re looking for a cozy morning treat you can feel good about, these coffee cake muffins are perfect. Grab a protein coffee and make them with me!


“AMAZING! My test is always, “If I ordered this in a bakery, would I be happy with it?” A definite YES! Super, super delicious! And even my spouse loves them! So good with a cup of coffee in the morning!”
-Brighton
Ingredients & Substitutions
Here I explain the best ingredients for my coffee cake muffin recipe, what each one does, and substitution options. For measurements, see the recipe card.
Muffin Base:
- Wholesome Yum Blanched Almond Flour – The main ingredient. I highly recommend this one because it’s finer than other brands, making the muffins soft and tender rather than grainy.
- Besti Monk Fruit Allulose Blend – This natural sweetener makes the coffee cake muffins ultra moist and tastes like sugar with no aftertaste. Other sweeteners can work okay, but won’t have these benefits. If you use something else, make sure to check my sweetener conversion chart for the right amounts.
- Unsalted Butter – For richness and buttery flavor. I like this brand. The closest substitute is coconut oil.
- Eggs – For structure and lift. Egg substitutes should work fine here if needed, but your muffins won’t be quite as fluffy.
- Heavy Cream – Makes these coffee cake muffins soft and tender. For something a little lighter, swap in milk, half-and-half, or full-fat coconut milk. You can also get a similar effect with sour cream instead.
- Baking Powder (for lift), Sea Salt (for balance), & Vanilla Extract (for flavor)
Cream Cheese Filling:
- Cream Cheese – Make sure it’s softened at room temperature before you start, so it blends smoothly without lumps.
- Besti Powdered Monk Fruit Allulose Blend – I highly recommend this powdered sweetener in the filling because it dissolves easily. Only regular powdered sugar will do the same, pretty much anything else can crystallize and leave the filling gritty.
- Vanilla Extract (for flavor again!)
Streusel Topping:
- Wholesome Yum Blanched Almond Flour – I use the same one here to keep the streusel crumbly and soft, while still holding together nicely.
- Besti Brown Monk Fruit Allulose Blend – It smells, tastes, and packs just like brown sugar, giving the streusel that classic flavor. The only close alternative with this kind of moisture is real brown sugar.
- Flavorings – Cinnamon is the star here, with a pinch of salt and vanilla for final touches.
- Unsalted Butter – Brings the streusel together and creates those crumbly tops.

How To Make Coffee Cake Muffins
I have step-by-step photos here to help you visualize the recipe. For full instructions with amounts and temperatures, see the recipe card.
- Make the cream cheese filling. In a bowl, beat together the cream cheese, powdered Besti, and vanilla, until smooth and creamy.
- Shape and chill. Transfer the mixture onto a sheet of plastic wrap, roll it into a long, thin log, and twist the ends. Freeze until firm.


- Mix the muffin batter wet ingredients. In a large bowl, beat the butter and Besti until fluffy. Then, mix in the eggs, cream, and vanilla.
- Add the dry ingredients. Beat again until smooth and thick.


- Make the streusel. In a separate bowl, stir together the almond flour, Besti Brown, cinnamon, and sea salt. Mix in the melted butter and vanilla, until a crumbly mixture forms.
- Fold together. Sprinkle some of the crumb topping over the batter and gently fold it in. Leave streaks so you get a layered look.


- Assemble the muffins. Spoon some batter into each cup of your prepared muffin pan, add a slice of the frozen cream cheese filling in the center, then top with the remaining batter. Crumble the rest of the streusel over the tops.
- Bake. Pop the coffee cake muffins in the oven, until the tops are golden. You can also use a toothpick to test, but be careful not to stick it into the cream cheese.



My Recipe Tips
- Bring your eggs and cream to room temperature before you start. If they’re too cold, the butter can firm up and create little clumps.
- The cream cheese roll doesn’t need to be frozen solid. I just freeze it until firm, which usually takes about 30 minutes.
- I recommend lining your muffin pan. I usually use these parchment cupcake liners, but lately I’ve been loving these silicone muffin liners because they’re reusable and dishwasher-safe.
- Avoid overfilling, or the coffee cake muffins can spill over as they bake. They don’t rise as much as traditional muffins, but you still need a little space. I fill each cup about halfway before adding the cream cheese, then top with more batter until just full.
- To keep these moist, don’t overbake. They’re done when a toothpick or fork inserted into the muffin part (not the cream cheese center) comes out clean.
- Be careful not to let the tops get too dark. If they brown before they’re done inside, I cover them loosely with foil and continue baking.
- Want more filling in every bite? Double the amount of cream cheese filling. A reader recommended this to me and I enjoyed the result when I tried it!
- For the best texture, let the muffins cool from hot to warm, but not totally cold. Letting them sit for 10-15 minutes is my ideal target. Waiting a bit improves the texture of the main muffin part, but the filling is still warm enough to be melty. You can also reheat these gently in the oven at 300 degrees F to get that melty center after cooling.

Coffee Cake Muffins (9g Protein!)
My easy, healthy coffee cake muffins have a cream cheese filling, cinnamon streusel topping, 9 grams of protein, and no refined sugar.
Ingredients
[ See substitutions ]Tap underlined ingredients to see the ones I use.
Cream Cheese Filling:
Muffin Base:
Streusel:
Instructions
[ See step photos See my tips ]Tap on the times in the instructions to start a kitchen timer.
Cream Cheese Filling:
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In a deep medium bowl, combine the cream cheese, Besti, and vanilla. Use a hand mixer to beat until smooth.
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Transfer the cream cheese mixture onto a sheet of plastic wrap, and wrap in a long, thin log shape, twisting the ends.
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Freeze for at least 30 minutes.
Muffin Batter:
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Meanwhile, in a large bowl, beat together the softened butter and Besti until fluffy.
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Beat in the eggs, then the cream and vanilla.
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Beat in the almond flour, baking powder, and sea salt, until uniform. The batter will be thick.
Streusel:
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In a medium bowl, stir together the almond flour, Besti Brown, cinnamon, and sea salt until uniform.
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In another small bowl, stir together the melted butter and vanilla.
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Add the melted butter mixture to the brown sugar mixture and stir until crumbly.
Assembly:
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Preheat the oven to 325 degrees F (162 degrees C). Line a muffin tin with 12 parchment paper liners.
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Sprinkle 1 cup of streusel (or about 2/3 to 3/4 of the total amount) over the muffin batter. Use a rubber spatula to gently fold in, but do NOT stir or mix until uniform (you want streaks of streusel).
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Spoon the muffin batter into the muffin cups, filling a bit less than halfway full.
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Remove the cream cheese from the freezer. Slice the log into 12 slices (about 2 teaspoons each). Place a slice in the center of each muffin cup.
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Spoon the remaining batter over the muffin cups, filling them to the top.
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Crumble the remaining streusel over the muffins, about 2 teaspoons per muffin.
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Bake for about 22-28 minutes, until the streusel is darker golden and an inserted toothpick comes out clean. If the muffins start to brown too much, tent the top with foil and continue baking until done.
Did you make it? Leave a review or tag me @wholesomeyum on Instagram!
Maya’s Recipe Notes
Serving size: 1 muffin
- Tips: Check out my recipe tips above to help you get the best moist texture in these coffee cake muffins and avoid common issues.
- Storage: Keep the muffins in an airtight container for 2-3 days at room temperature or up to a week in the fridge.
- Meal prep: Make them ahead, or just prep the filling and topping in advance.
- Freeze: Store in an airtight container or zip lock bag for up to 3 months. You can thaw on the counter or in the fridge overnight.
I provide nutrition facts as a courtesy. Have questions about calculations or why you got a different result? Please see my nutrition policy.
Add Your Notes Your Notes
© Copyright Maya Krampf for Wholesome Yum. Please DO NOT SCREENSHOT OR COPY/PASTE recipes to social media or websites. We’d LOVE for you to share a link with photo instead.
Coffee Cake Muffins

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52 Comments
Andrew & Diane
1Hi Maya. I really liked this recipe. The muffins came out great and the cinnamon swirl was good. I’m really sold on the Besti Monk Fruit/ Allulose sweetener. The cream cheese mixed with that tasted great with no after taste. When I used Truvia in a previous receipt for icing, you could get an objectionable after taste, but not with the Monk fruit. Thanks for a great recipe. And my wife thanked you when she woke up to my usual kitchen disaster. LOL. Andy
Ruth
1The directions are confusing. My husband loved them, he gave you 5 stars . I thought they were good, but I didn’t use the same brands of sweetners. That may have changed the flavor.
Theresa Mast
0Mealy grainy texture. Not my favorite.
Maya | Wholesome Yum
0Hi Theresa, Oops, sounds like you likely used the wrong almond flour or sweetener! Many brands can cause this, which is why I created and recommended specific ones that avoid this issue.
Sue
0I agree with everyone else….you cannot tell these are Keto, they taste so wonderful! They are best right out of the oven tough, so I’d warm them up if you use them later. Next time I might add some nuts to the streusel. However, they were great without them. We will be making these again!
Wholesome Yum D
0Sue, I love hearing that! Warm right out of the oven really is the sweet spot, and nuts in the streusel sounds like such a cozy twist. So glad these will be a repeat for you.
pam
0yes…YUM!
Maya | Wholesome Yum
0I’m glad you liked these, Pam!
Jessica
0Hii, can’t wait to make these today, since they have cream cheese will they need to be stored in the fridge?
Maya | Wholesome Yum
0Hi Jessica, Yes, store them in the fridge since they have cream cheese.
Susan
0These muffins were moist and delicious. The texture was equivalent to a regular coffee cake muffin. The only thing I would change would be to add a little bit more cream cheese filling in the center. I doubled mine and they were perfect. This will definitely be something I bake again!
Laurie
0Amazingly delicious!! I’d take these over a donut anyday! Just remember that if you’re trying to lose weight, these are pretty high in calories. 😉
Stefanie
0I need almond flour recipe but cannot do any type of artificial sweetener. Can I substitute regular sugar 1:1 in this recipe?
Wholesome Yum D
0Hi Stefanie, yes, Besti Monkfruit Allulose Blend measures 1:1 with real sugar.
Arianna
0So far they have turned out great I was wondering why my filing wouldn’t freeze?
Wholesome Yum D
0Hi Arianna, You want to freeze until the filling is just firm, not frozen solid.
Katie Johns
0These are the best muffins I’ve ever cooked. Awesome recipe! ❤️ ??
Ashley
0Thank you so much for this recipe!! I can’t even tell it’s keto!! They are absolutely amazing!!
Joanne Famularo
0These came out amazingly delicious. So nice to have a decent Keto dessert with my coffee now.
Michelle A.
0Question – I notice there seems to be very little cinnamon in the recipe even though they are cinnamon muffins. I’m wondering is it a mild/hint of cinnamon flavor in these? Maybe a little more vanilla or like a mild coffee-cake? Or does the cinnamon really come through strong? They sound really good as-is, but sometimes I like to be “punched in the face” with cinnamon flavor so might consider adding more to the batter itself and maybe the cream cheese too if the flavor is mild as written. Do you think adding extra cinnamon in the other components would hurt anything or throw off the ratios if I try it?
Wholesome Yum D
0Hi Michelle, You could add in extra cinnamon if you like the bold flavor.
Susan Odiseos
0I have your Wholesome Yum almond flour and sweeteners. My question for dairy free: will it work to use dairy free cream cheese and coconut milk in place of heavy cream? I fear too much will be lost in taste, but eager to know. Thank you.
Wholesome Yum D
0Hi Susan, I have never used vegan cream cheese in this recipe but it should work along with the coconut milk.
Sabina Coyle
0Fantastic recipe!!
Sharon
0Absolutely delicious. Will be making it again today as they were such a hit.
I substituted xylitol for some of the sugar as that is my favorite.
Can’t wait to do October ones with pumpkin in the cream cheese.
Jean
0Love, love these muffins! Unfortunately, I had to adapt it with half cane sugar and half sugar substitutes.
Do you happen to have the equivalent amount of a sugar substitute other than monk fruit, or allouse, or stevia? I’m having mild to moderate allergic reactions to all of these. I’m trying theses natural sugar substitutes to go on keto but seem to be very allergic.
Wholesome Yum M
0Hi Jean, You can use this Sweetener Calculator to find the correct equivalents. Sugar is on the list, so you can quickly tell how sweet is sweetener is compared to sugar.
Jean
0Thank you!:)
Sara
0Wow, wow, wow, is all I can say! These muffins are delicious! A bit time consuming, making the filling, batter, and streusel, but well worth the time investment. They’re decadent and filling. I had to hide some from my friend so she didn’t steal them all, and I would have included a picture here, but they disappeared so quickly. I’m already thinking of a blueberry version with a lemon cream cheese filling. Can’t wait to give it a try.
Barbara Kawulich
0This recipe is a keeper! It was quite a bit of work, but they taste delicious, and it was worth it. I had to taste one to make sure they were done, and oh, yummy! I extended the cook time by 5 minutes, as the toothpick kept coming out wet. I also added pecans to the streusel. Delicious! Thanks for sharing this recipe.