Starbucks Keto Pumpkin Cream Cheese Muffins
Published November 4, 2021 • Updated March 15, 2026
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I gave up the Starbucks pumpkin muffin when I went keto and thought that was it. This low carb copycat brought it back. Brown butter batter wraps around a vanilla cream cheese center that tastes exactly like the original.
I started making these in 2018 after realizing I could get the same brown butter pumpkin flavor without the 53 grams of carbs from the Starbucks original. The muffin part came together fast. The filling took three tries. Too thin and it melts into the batter. Too thick and it sets up chalky. The ratio in this recipe holds its shape and tastes like actual frosting, which is the whole point of having a filled muffin.
Brown butter is the step that makes everything work here. I tested a batch without it once, and the muffins tasted flat. Just plain pumpkin with sweetener. The browned butter adds a nutty, almost caramel depth that rounds out the spice and makes the whole thing taste less like a diet swap and more like something from a bakery. Five extra minutes at the stove. I will never skip it.
One thing I learned the hard way: let the browned butter cool before mixing it into the batter. If it’s still warm when you pipe in the filling, the center softens too fast and merges into the pumpkin instead of staying as a distinct layer. Room temperature batter, cold filling. That’s what makes the center hold.
These freeze well. I make a double batch, wrap individually in plastic wrap, and pull one out whenever I want a quick keto breakfast. Microwave for 30 seconds and the center comes back just right. I keep them in the freezer for up to three months with no texture loss. If you like batch-prepping keto breakfasts, my keto pumpkin pecan muffins freeze the same way.
If coconut flour gives you trouble (it makes some people’s baked goods dense and gummy), you can swap it for all almond flour. It’s not 1:1 since coconut absorbs way more liquid. I’d add about 3/4 cup extra almond flour to replace the coconut portion and pull back on the pumpkin puree by 2-3 tablespoons. Haven’t done that exact swap in this recipe, but that’s where I’d start based on how my other almond-flour-only muffins have turned out.
For mornings when I want something sweet instead of bacon and eggs, these and a cup of coffee are it. If you want more options, my keto cream cheese danish hits a similar spot, and almond flour pancakes are great when I have an extra ten minutes.
How to Make Copycat Starbucks Pumpkin Muffins
I bake these at 325, which is lower than most muffin recipes. The slower bake lets the outside set without overcooking the filling inside. Mine are usually done around 45 minutes, but I start checking at 40. The tops should be golden and spring back slightly when you press them. If they’re still pale at 45 minutes, give them a couple minutes under the broiler for color. Let them cool completely in the pan before removing or the centers will be too soft to hold.
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Keto Pumpkin Muffins Ingredients
1/2 cup unsalted butter -
1 1/2 cups almond flour
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1/2 cup coconut flour
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2 teaspoons baking powder
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1 teaspoon baking soda
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1 1/4 teaspoon salt
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2 teaspoons cinnamon
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1/2 teaspoon turmeric
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1/4 teaspoon nutmeg
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1 1/2 cups pumpkin puree
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3 eggs
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1/4 cup sugar free brown sugar
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1/2 cup sugar free maple syrup
Cream Cheese Filling Ingredients
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8 oz cream cheese, softened
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1/2 cup heavy cream
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1/4 cup sugar free sweetener
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2 teaspoon vanilla
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1/4 cup coconut flour
Step by Step Instructions
Step by Step Instructions
Make brown butter
Add butter in a small saucepan and heat over medium heat. Swirling occasionally, cook the butter until melted and starts to brown and smells nutty (about 5 minutes). Remove from the heat and set aside to cool.
Mix dry ingredients
Whisk together almond flour, coconut flour, baking powder, baking soda, salt, cinnamon, turmeric and nutmeg in a medium bowl. Set aside.
Mix wet ingredients
In a separate bowl, add eggs, pumpkin puree, sugar free brown sweetener and sugar free maple syrup. Beat with an electric mixer until smooth.
Combine all ingredients to muffin batter
To the wet ingredients, slowly mix in the dry ingredients and the browned butter. Mix until combined.
Add to muffin liners
Evenly add keto pumpkin muffin batter to the muffin liners. Fill close to the top as keto muffins don’t rise very much.
Make cream cheese filling
To a small bowl, add softened cream cheese, heavy cream, sugar free sweetener, vanilla and coconut flour. Mix with an electric mixer until smooth and creamy. Add to a piping bag and ziploc bag with a large piping hole.
Pipe cream cheese filling into the center
Pipe about 2 tablespoons of cream cheese filling into the center of the muffin batter. Basically fill until the filling reaches the top of each muffin batter in the liner.
Nutrition disclaimer
The nutrition information provided is an estimate and is for informational purposes only. I am a Doctor of Pharmacy (Pharm.D.); however, this content is not intended to be a substitute for professional medical advice, diagnosis, or treatment. Always consult your physician or other qualified health provider before making any lifestyle changes or beginning a new nutrition program.
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Get My Macros + Recipes →Frequently Asked Questions
Can I swap coconut flour for all almond flour?
I've done this in other muffin recipes and it works, but it's not a 1:1 swap. Coconut flour absorbs way more liquid than almond flour. I'd use about 3/4 cup extra almond flour to replace the coconut portion and reduce the pumpkin puree by 2-3 tablespoons. Start there and adjust if the batter looks too wet or too dry.
How do I reheat these from frozen?
I freeze mine individually wrapped in plastic wrap, and they keep for up to three months. When I want one, I microwave it for 30 seconds straight from the freezer. The filling in the center comes back creamy and the muffin warms through without drying out. No need to thaw first.
Why is the filling sinking into the batter instead of staying in the center?
This happens when the batter is too warm. If you mix in the browned butter and immediately pipe in the filling, the heat softens it and it merges into the pumpkin. I let my batter cool to room temperature before piping. Also make sure your filling is thick. If it's runny, add an extra tablespoon of coconut flour to stiffen it up.
Can I make this as a loaf or cake instead of muffins?
I haven't tested this as a loaf, but a reader of mine made a doubled batch in a 9-inch cake pan and it worked well. I'd give it an extra 8-10 minutes of bake time and tent with foil if the top browns too fast. Swirl the filling on top rather than piping it in so you get a visible layer.
Can I make mini muffins with this batter?
I haven't tried minis with this specific recipe, but the batter would work in a mini muffin pan. I'd reduce the bake time to about 18-22 minutes and pipe a smaller amount of filling into each one (maybe a teaspoon instead of two tablespoons). Watch them closely since minis go from done to overdone fast.
What can I use instead of sugar-free brown sugar?
I swap in granulated erythritol or monk fruit sweetener when I'm out of sugar-free brown sugar. Use a 1:1 ratio. You lose a tiny bit of the molasses depth that brown sugar adds, but the pumpkin spice and browned butter cover for it. My batches with regular keto sweetener still taste great.
Are these gluten-free?
Yes. I use almond flour and coconut flour, so there's no gluten in these. If you have a nut allergy, this recipe won't work for you since almond flour is the main structure. I haven't found a nut-free version that holds up the same way.
How long can I store these?
I keep mine in an airtight container at room temperature for up to 3 days, or in the fridge for about a week. For longer storage, I freeze them individually wrapped for up to 3 months. The texture holds up well either way, though I think they taste best at room temperature or warmed up for a few seconds.
Used to get these every fall at Starbucks before I went keto, and I stopped thinking about them after a while. Made a batch on Sunday and the brown butter smell took me right back. Nice to have that again.
The cream cheese filling was good on its own but I added a tiny pinch of cinnamon to it before piping and it made a real difference. Both layers tasted like they belonged together instead of one pumpkin muffin with a separate vanilla situation in the middle. Total beginner instinct, but it worked. Also learned the hard way that the batter needs to be fully cooled after adding the browned butter or the cream cheese softens too fast when you try to layer it in.
I gave up Starbucks pumpkin muffins when I started keto and genuinely thought that was just something I'd left behind forever. Made these last Sunday and the brown butter in the batter was what got me, it adds this depth and almost nutty richness that makes the whole thing taste less like a diet compromise and more like something you'd actually seek out. I was a little nervous about piping the cream cheese filling into the center but it worked on the first try and the payoff is worth the extra step. Pulled one out still warm and the inside was this dense, moist pumpkin cake with a cool vanilla center and I just kind of stood in my kitchen for a second. I've been doing this almost two years and I still get caught off guard when something hits that hard. Going back for a second batch this weekend, probably double so I can freeze some.
Two years and it still stops you. Yeah. Double batch and freeze - pull one out and microwave 30 seconds, the cream cheese center comes back just right.
I went keto in January and the Starbucks pumpkin muffin was the first thing I actually mourned. Made these on a snow day this week and the brown butter smell alone was worth it, but that cream cheese center is exactly what I remembered. Not over it.
Snow day was the right call for these. Brown butter smell gets me every single time I make them.
I've tried probably six or seven keto pumpkin muffin recipes and the cream cheese filling is always where they fall apart. Either it's too runny, sets up chalky, or just merges into the batter so you can barely tell it's there. Not here. The filling held its shape and tasted like actual cream cheese frosting, which is the whole point. The brown butter was a step I almost skipped (felt like extra dishes on a Tuesday night) but it does something to the flavor I can't explain. Without it, my other attempts just taste flat. One thing: the tops were still pale when the toothpick came out clean at 325, so I gave them two minutes under the broiler for color. Four stars, but that's my oven running cool, not the recipe.
The broiler fix works. Two minutes does it. Brown butter is the one step I'd never cut. Tested without it once and the batch just tasted flat.
Coconut flour always makes my muffins dense and gummy, so I want to swap it for all almond flour. Straight 1:1 swap, or do I need to adjust the liquid too since coconut absorbs so much more?
Not 1:1, yeah - coconut flour absorbs way more. I'd add about 3/4 cup extra almond flour to replace it and pull back on the pumpkin puree by 2-3 tablespoons. Haven't done that specific swap in this recipe but that's where I'd start.
WOW these are absolutely delicious and completely worth making!
Thank you for the recipe!
Ha, the brown butter smell does that to me too. Always make a double batch. They go fast.
I’m thinking I may make this in a 9 inch cake pan doubling the recipe then swirling the cream cheese mixture into batter or spreading cream cheese frosting on top.
Swirl over frosting. The cream cheese is thick enough it won't sink down. Give it an extra 8-10 minutes in the 9 inch pan and tent with foil if the top browns too fast.
These are really yummy.
The cream cheese center is what makes it. Took three tries to nail the ratio.
Sorry I meant coconut flour not powder.
Haven’t tried these yet but you say protein powder in your video and in the ingredient list it shows coconut powder. Does it make a difference in the baking?
You can actually use either. Both will work. The protein powder will probably make them puff up more.