Healthy Pumpkin Cookies
Published October 21, 2025 • Updated February 20, 2026
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I make these healthy pumpkin cookies soft, chewy, and loaded with over 16g of protein per cookie. Topped with a tangy cream cheese frosting, they're my sugar-free Crumbl copycat with only 4g net carbs.
These aren’t your typical pumpkin cookies. They’re high in protein, completely sugar-free, and still soft, chewy, and cozy enough to make you forget they’re good for you. I wanted a healthy fall cookie that tastes indulgent (like something you’d grab from Crumbl) but without the sugar crash. These are the kind I bake every fall and keep in the fridge all week.
What makes these different
- The texture. Most recipes like this rely on oats, nut butter, or maple syrup for chew. Mine use Greek yogurt and protein powder for softness and structure without the carbs. If you’ve made my almond flour cookies, you know I’m particular about that balance between chewy center and slightly set edges.
- The macros. Because I skipped the oats and nut butters, you get a cookie that’s genuinely low in carbs without extra fat or sugar to compensate. Unlike most low-carb cookies that turn out dry or crumbly, these hold together with real chew in the center. Each one has over 16 grams of protein and only 4 net carbs.
- The frosting. I make a cream cheese frosting with Greek yogurt and a scoop of whey instead of powdered sugar or butter. It’s light, fluffy, and tangy. I ate this frosting by the spoonful more than once while testing. If you like cream cheese frosting, try it on my keto pumpkin whoopie pies too.
The base uses almond flour and oat fiber instead of traditional flour, which keeps them tender without a gritty texture. If you’re new to baking with almond flour, my keto chocolate chip cookies are another great starter recipe with a similar base.
One thing I’ve learned from making these over and over: I actually prefer them straight from the fridge. The cream cheese frosting firms up and takes on this dense, almost cheesecake-like texture that I can’t get enough of. One of my readers, Maria, described it as a “cheesecake vibe,” and she nailed it.
If you’re into pumpkin season baking, these pair well with my keto pumpkin chocolate chip cookies or keto pumpkin cheesecake. And if you want more sugar-free desserts that don’t taste like diet food, my low calorie brownies and keto no bake cookies are two I come back to constantly.
If you’re craving that classic Crumbl cookie vibe but want something that fits your macros, this is it. No sugar, no flour. Just a batch of cozy, fall cookies that feel indulgent and intentional.
How I make these cookies
The whole batch takes about 30 minutes: mix the dough, scoop, bake, and frost. The dough is forgiving and scoops cleanly, so I find it’s great for making with kids or prepping ahead for the week.
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Pumpkin Protein Cookies Ingredients
1/3 cup plain Greek yogurt -
1/2 cup pumpkin puree
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1/4 cup sugar-free sweetener
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1 large egg
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1 teaspoon vanilla extract
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1 cup almond flour
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1 tablespoon oat fiber
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1 scoop (29g) whey protein powder
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1/2 teaspoon baking powder
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pinch of salt
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1 teaspoon pumpkin pie spice
Cream Cheese Frosting Ingredients
-
4 oz cream cheese, softened to room temperature
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1/4 cup plain Greek yogurt
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1 scoop (29g) whey protein powder
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2 tablespoons sugar-free sweetener
Step by Step Instructions
Step by Step Instructions
Mix wet ingredients
In a large bowl, add yogurt, pumpkin puree, sweetener, egg and vanilla extract. Mix together until smooth.
- 1/3 cup plain Greek yogurt
- 1/2 cup pumpkin puree
- 1/4 cup sugar-free sweetener
- 1 large egg
- 1 teaspoon vanilla extract
Stir in dry ingredients
Then add almond flour, oat fiber, protein powder, baking powder, salt and pumpkin pie spice. Mix until combined.
- 1 cup almond flour
- 1 tablespoon oat fiber
- 1 scoop (29 g) unflavored whey protein powder
- 1/2 teaspoon baking powder
- pinch of salt
- 1 teaspoon pumpkin pie spice
Scoop & bake
Using a large cookie scoop (one that holds 2 tablespoons), scoop cookie dough onto a parchment lined baking tray. Bake the cookies for 15-18 minutes or until they are set on top. Remove from the oven and let cool.
Cream cheese frosting
Make the frosting while the cookies are cooling. In a small bowl, combine cream cheese, yogurt, protein powder and sweetener until light and fluffy. Spread the frosting on top of the cooled cookies and dust on more pumpkin pie spice.
- 4 oz cream cheese, softened to room temperature
- 1/4 cup plain Greek yogurt
- 1 scoop (29 g) unflavored whey protein powder
- 2 tablespoons sugar-free sweetener
- pumpkin pie spice (for dusting)
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
What can I use instead of oat fiber?
I've tested coconut flour as a swap, and it works, but use about half the amount since it absorbs way more liquid. You can also try psyllium husk powder (about 1 teaspoon) for a similar binding effect. My preference is still oat fiber because the texture is closest to what I get with the original recipe, but coconut flour is my go-to backup.
Can I make these dairy-free?
I haven't tested a fully dairy-free version myself, but the swaps are straightforward. Use a thick coconut or almond yogurt in the dough and a dairy-free cream cheese for the frosting. The biggest thing to watch is moisture. Dairy-free yogurts tend to be thinner, so add an extra tablespoon of almond flour if the dough feels too loose.
How many calories are in each cookie?
Each frosted cookie comes out to 262 calories, 16.8g protein, 18.8g fat, and 4.2g net carbs. Without the frosting, you're looking at roughly 180 calories and about 10g protein. I think of these as a better macro profile than most protein bars, and they actually taste like a real cookie.
Can I use casein protein instead of whey?
One of my readers, David, tried casein in the frosting and said it came out thicker, almost like a buttercream. I thought about it and it makes sense. Casein sets up firmer than whey, so the frosting holds its shape better, especially in the fridge. I'd still use whey in the cookie dough itself (casein can make baked goods a bit dense), but casein in the frosting is a solid move.
Are these actually keto?
With 4.2g net carbs per cookie, they fit within a standard keto target of 20-30g net carbs per day. The carbs come from almond flour and pumpkin puree, both whole food sources. I eat two of these in a sitting sometimes and it barely dents my daily carb count.
Can I skip the frosting?
The cookies taste great on their own, especially warm out of the oven. Without frosting, each cookie drops to roughly 180 calories and about 10g protein. I make unfrosted batches when I'm doing meal prep because they stack better in containers. But the frosting is where the extra protein boost comes from, so I usually add it when I'm eating them fresh.
How do these compare to a Crumbl cookie?
A typical Crumbl cookie runs 500+ calories, 60g+ carbs, and 40g+ sugar. Mine have 262 calories, 4.2g net carbs, and zero sugar. I designed the recipe specifically to mimic that Crumbl chew (Greek yogurt and protein powder do the work that butter and sugar usually handle), so the texture is closer than you'd expect.
Can I freeze these?
I freeze these all the time. My method: freeze them unfrosted in a single layer on a sheet pan, then transfer to a freezer bag once solid. They keep for up to 2 months. When I'm ready to eat them, I thaw in the fridge overnight and add the frosting fresh. The frosting doesn't freeze well (it gets grainy), so always frost after thawing.
Made a batch last weekend. Pretty good overall, but mine spread totally flat instead of staying thick like the photos. Used the large scoop, baked at 350. Is that usually a protein powder brand thing or should I chill the dough first?
I've made every version of keto pumpkin cookies at this point and most of them end up cakey in a way that reads more like muffin tops than cookies. This one is actually different. The protein powder and Greek yogurt combination does something to the texture that the almond-flour-only recipes can't touch, it holds together with this soft chew that stays that way even after a day in the fridge. The cream cheese frosting is what sold me completely, tangy enough to cut through the sweetness without being overpowering. I was honestly skeptical it would come close to a Crumbl cookie but the size and the frosting ratio are spot on. 16g of protein per cookie is the part that keeps pulling me back to this recipe over every other version I've tried. I'm already making a second batch this weekend.
My daughter grabbed one before I finished frosting the batch and said they smelled like fall (her words, in March). The frosting just barely covers 6 cookies, so I'd make 1.5x next time, but the pumpkin spice is strong enough you don't need it.
Ha, 'smells like fall' in March is a win. And yeah, I always make extra frosting. 1.5x covers 6 cookies cleanly.
First time actually trying keto baking, and I grabbed this one on a whim during a snow day. The dough came together so fast (the Greek yogurt helps, I think?), and the cookies came out soft and almost pillowy, not the dense texture I was bracing myself for with almond flour. That cream cheese frosting on top was really the thing that got me. Quick question: do you think vanilla protein powder would work here? I can't find unflavored near me.
Vanilla works fine. The dough already has a teaspoon of vanilla in it, so you're just leaning into that. If it's sweetened vanilla powder, back off a tiny bit on the sweetener in the dough.
Can I freeze these? Want to meal prep a batch but not sure if the cream cheese frosting holds up after thawing.
Yes, I freeze these all the time. I actually freeze them unfrosted and add the cream cheese frosting after thawing. Holds up better that way.
My kids inhaled these. They had no clue there was protein powder in them.
Ha, same here. I've learned not to mention the protein powder until after they've eaten them.
The cream cheese frosting is the real star here. It firms up in the fridge and gets this dense cheesecake vibe.
Yeah the cold frosting is the best part. I actually prefer them straight from the fridge for that reason.
Used casein protein instead of whey in the frosting. Came out thicker, almost like a buttercream. Liked it better.
Oh that's smart. Casein sets up firmer, makes sense it'd get that buttercream texture. Might actually hold up better in the fridge too.