Home » breads 'n biscuits » Keto Pumpkin Spice Latte Cupcakes (or Muffins!) 🎃🍂☕

Keto Pumpkin Spice Latte Cupcakes (or Muffins!) 🎃🍂☕

Got PSL fever?! These gluten free and keto pumpkin spice latte cupcakes (or muffins!) are deliciously moist, totally aromatic and got a killer crumb! Note: this recipe has since been updated to yield even fluffier (and easier) cupcakes. 

Gluten Free & Keto Pumpkin Spice Latte Muffins (or Cupcakes!) #keto #lowcarb #healthyrecipes #glutenfree #pumpkin #pumpkinspicelatte #muffins #cupcakes
Gluten Free & Keto Pumpkin Spice Latte Muffins (or Cupcakes!) #keto #lowcarb #healthyrecipes #glutenfree #pumpkin #pumpkinspicelatte #muffins #cupcakes

Keto Pumpkin Spice Latte Muffins

Or Cupcakes!

This recipe comes with a heartfelt dedication to all you pumpkin spice latte lovers out there! 😉

Because these guys right here are just totally aromatic (hello coffee and pumpkin pie spice!), extra fluffy and with a killer moist crumb (had to be said!). 

So whip them up solo (think the best keto coffee muffins!), fill them up with our pumpkin cream cheese filling (my favorite!), top with almond streusel, or finish them up with our cream cheese buttercream frosting (I was feeling a little bit extra…!). 

i.e. you’ve got 6 topping and filling permutations at your disposal.

Having said that, I cannot recommend enough that you whip up the pumpkin cream cheese filling. It’s really takes these guys completely over-the-top!

Gluten Free & Keto Pumpkin Spice Latte Muffins (or Cupcakes!) #keto #lowcarb #healthyrecipes #glutenfree #pumpkin #pumpkinspicelatte #muffins #cupcakes
Gluten Free & Keto Pumpkin Spice Latte Muffins (or Cupcakes!) #keto #lowcarb #healthyrecipes #glutenfree #pumpkin #pumpkinspicelatte #muffins #cupcakes
Gluten Free & Keto Pumpkin Spice Latte Muffins 🎃🍂☕
Gluten Free & Keto Pumpkin Spice Latte Muffins (or Cupcakes!) #keto #lowcarb #healthyrecipes #glutenfree #pumpkin #pumpkinspicelatte #muffins #cupcakes

The Pumpkin Pie Spice

You seasoned bakers probably know this already, but nutmeg is one of those spices (like pepper!) that is always best freshly grated.  

So for something like pumpkin spice, where nutmeg is key, I would highly suggest going the homemade route.

But if need be, Simply Organic makes a solid one (and lol, you can always tell its PSL season when Amazon is running low on stock…!).

Paleo & Keto Pumpkin Spice Latte #keto #lowcarb #healthyrecipes #dairyfree #glutenfree #paleo #pumpkin #pumpkinspicelatte
Paleo & Keto Pumpkin Spice Latte #keto #lowcarb #healthyrecipes #dairyfree #glutenfree #paleo #pumpkin #pumpkinspicelatte
Gluten Free & Keto Pumpkin Spice Latte Muffins (or Cupcakes!) #keto #lowcarb #healthyrecipes #glutenfree #pumpkin #pumpkinspicelatte #muffins #cupcakes
Gluten Free & Keto Pumpkin Spice Latte Muffins (or Cupcakes!) #keto #lowcarb #healthyrecipes #glutenfree #pumpkin #pumpkinspicelatte #muffins #cupcakes

The Flours

The keto coffee muffins use a mix of super fine almond flour, psyllium husk, golden flaxseed meal and a touch of xanthan gum. (See links for specific brands I use and love). 

Just keep in mind that for best texture and rise, you’ll always want to regrind your golden flaxseed meal in a dry blender or bullet. And be sure you’re either using either very finely ground psyllium powder or to regrind your husks!

Oh, and golden flaxseed isn’t the same as normal flaxseed (which results in gummy and dense baked goods).

Gluten Free & Keto Pumpkin Spice Latte Muffins (or Cupcakes!) #keto #lowcarb #healthyrecipes #glutenfree #pumpkin #pumpkinspicelatte #muffins #cupcakes
Gluten Free & Keto Pumpkin Spice Latte Muffins (or Cupcakes!) #keto #lowcarb #healthyrecipes #glutenfree #pumpkin #pumpkinspicelatte #muffins #cupcakes

The Sweetener

You’ve got good options here! Allulose is my favorite for best texture and no aftertaste now (you do need to add 30% more though), Lakanto Golden (baked goods with erythritol can have a slight hard texture, still not big deal here though), xylitol (non-corn though to avoid tummy troubles!).

Pyure (an erythritol and stevia blend) is also a good one for muffins and quick breads, particularly if you’re trying to limit your sugar alcohol consumption (it’s added stevia makes it twice as sweet as sugar… i.e. you add half!).

Oh, and if not restricted by sugars, simply sub 1-to-1 with coconut or regular sugar.

If you’re opting for the buttercream frosting (which comes highly recommended!), your best options are allulose and xylitol (no aftertaste), followed by erythritol (some cooling effect). But they must be powdered.

So get your blender out, make sure it’s completely dry, and process your sweetener of choice until powdered. Just make sure you wait a few moments for the dust to settle before opening the blender or food processor.

Or you can always grab a bag of Lakanto powdered or Swerve confectioner’s.

And if using xylitol, make sure to be careful if you have a pup (or kitty!) around the house, as it’s highly toxic to the little guys! 🐕

Gluten Free & Keto Pumpkin Spice Latte Muffins (or Cupcakes!) #keto #lowcarb #healthyrecipes #glutenfree #pumpkin #pumpkinspicelatte #muffins #cupcakes
Gluten Free & Keto Pumpkin Spice Latte Muffins (or Cupcakes!) #keto #lowcarb #healthyrecipes #glutenfree #pumpkin #pumpkinspicelatte #muffins #cupcakes
Gluten Free & Keto Pumpkin Spice Latte Muffins
Gluten Free & Keto Pumpkin Spice Latte Muffins

Gluten Free & Keto Pumpkin Spice Latte Muffins (or Cupcakes!) #keto #lowcarb #healthyrecipes #glutenfree #pumpkin #pumpkinspicelatte #muffins #cupcakes

Gluten Free & Keto Pumpkin Spice Latte Cupcakes (Or Muffins!)

Got PSL fever?! These gluten free and keto pumpkin spice latte cupcakes (or muffins!) are deliciously moist, totally aromatic and got a killer crumb!
Oh, and if baking with cups rather than grams is your thing, just click on US Cups for an instant conversion.
5 from 38 votes
Prep Time 10 minutes
Cook Time 20 minutes
Total Time 30 minutes
Course Dessert
Cuisine American, Keto
Servings 6 cupcakes
Calories 130 kcal


For the keto pumpkin spice latte muffins

For the pumpkin spice filling (optional)

For the frosting (optional)

For the almond streusel (optional)


For the keto pumpkin spice latte muffins

  • If making the filling, go ahead and whip it up first! Preheat oven to 350°F/180°C. Grease and flour a muffin tray (I find coconut flour to work best).
  • Add almond flour, flaxseed meal, psyllium husk, baking powder, pumpkin spice, xanthan gum and salt to a medium bowl. Whisk until thoroughly combined, set aside.
  • Add sweetener and eggs to a large bowl and beat with an electric mixer for 3-5 minutes until airy and lighter in color. With the mixer on, add in the vanilla extract, apple cider vinegar, coffee and butter.
  • Add in the dry flour mixture in two parts, alternating with the sour cream. Continue to mix for a minute or two until fully incorporated and elastic (the batter will thicken as you mix!).
  • Spoon batter onto the prepared muffin tray, evening out the top with the back of a wet spoon. If you are filling them up with the pumpkin filling: spoon batter 3/4 full, add a tablespoon pumpkin cream cheese and cover with a thin layer batter. Sprinkle with almond streusel (if using).
  • Bake for 23-27 minutes without filling and for 30-35 minutes with filling. Note: you guys have reported back on very large varying baking times for these (I'm thinking amount of filling and how cold said filling is), so I suggest ensuring yoru filling is at room temperature.
  • Allow to cool for 15 minutes in the pan before removing, and cool completely in a rack if frosting. Just note that these are best enjoyed fully cooled, once the flavors have had a chance to mingle!
  • Keep covered and refrigerated for up to 3 days, though I'm fairly certain they'll be long gone before then. Plus, they also freeze great!

For the pumpkin filling (optional)

  • Add pumpkin puree and cream cheese to a medium bowl. Cream together with an electric mixer until fully combined. Add in sweetener, vanilla extract and pumpkin pie spice until fully combined. Allow it to come to room temperature before baking it into the muffins (for best texture and rise).

For the almond streusel (optional)

  • Add almond flour, coconut flour, pumpkin pie spice, sweetener and salt to a food processor and pulse to combine. Add in butter and pulse until the mixture resembles bread crumbs. Add in pecans and pulse until roughly chopped and mixed in. If no food processor is on hand (or don't want to clean an extra appliance!), feel free to rub the butter in with your fingertips until crumbly in texture.
  • Cover and refrigerate until needed, and up to 5 days. 


Please note that nutrition facts below are for the pumpkin spice latte cupcakes only. Add 1g net carb for the pumpkin filling and 0.2g net carbs/serving for the cream cheese buttercream frosting


Serving: 1muffin | Calories: 130kcal | Carbohydrates: 4g | Protein: 4g | Fat: 14g | Saturated Fat: 6g | Cholesterol: 74mg | Sodium: 284mg | Potassium: 20mg | Fiber: 2g | Vitamin A: 315IU | Calcium: 38mg | Iron: 0.8mg
Keyword keto coffee muffins, keto pumpkin spice latte cupcakes
Whip up this recipe?Comment below or drop me a line @gnomgnom._ and tag #gnomgnomyum!


  1. rima sabbagh says:

    I’ve been keto for 3 years now. I bake weekly, not only was this recipe time consuming but it tastes very very bland. Will not make again.

  2. Margerette Burnette says:

    Hello…deff making these soon..was wondering if you had total macros for entire recipe? I am not sure on serving sizes to get macros.. thanks..

  3. Gwyneth says:

    5 stars
    I prepared the batter exactly as written, then placed in 16 mini silicone muffin cups with frozen pumpkin cheesecake middle, baked for 18 minutes. Perfect! Topped with your suggested frosting, they were so delicious, cannot thank you enough.

  4. Sherry says:

    5 stars
    Oh my – these are scrumptious! I made a batch this morning using frozen pumpkin cheesecake as suggested. They were baked for 25 minutes and are soft, moist, and out of this world. I didn’t frost or use the streusel (we don’t need the extra calories) and these are so good without anything else.

    I had shown my husband the picture from this site and asked if he liked pumpkin: affirmative! He is REALLY going to like these (if I can leave them alone until he gets home from work).

  5. Nicole says:

    So first of all, I make ALL of your recipes and they are always delicious — they’re staples in my house. But when I baked these for 20 minutes, they were nowhere near done. I left them in another 10 mins (I’m at sea level — no high altitude concerns) and let them cool for a few hours, then opened one up and….the muffin part is just not cooked at all. Is this because I put the filling in frozen? Maybe it needed a lot longer because the filling was trying to come to temp? I’m throwing them back into the oven for anotehr 20 minutes now, as I just can’t bear the thought of throwing the batch away but I also can’t eat the raw, unpasteurized eggs if the batch (okay, double batch!) stays raw-ish. Any thoughts or suggestions?

    • Paola says:

      Oh no Nicole! I’m sorry this happened to you! Ovens do vary a bit (and as you mention I’m at high altitude so things do bake faster), so maybe it was that? I’ll add a note to the recipe with your experience (and yup, you can pop them in the oven again 🙁

    • Nicole Renee Wimmer says:

      5 stars
      Thanks for the suggestion!
      I popped these back in the oven (ultimately doubled the baking time) — I’m at 0 ft. (sea level). And they were PERFECT, absolutely amazing!
      I’ve also made your blondies the other day (swoon to high heaven) and ended up doubling the baking time and they were just set in the middle.
      They both turned out SOOOO heavenly.
      Your recipes are the only ones I ever make anymore! So amazing.

  6. Michelle says:


    I love all your recipes. I was wondering, is there a way to convert this to an individual(i.e. Mug Cake)? I am the only one on the Keto diet and unfortunately a whole batch would go to waste.

    Thank you for all the hard work you do!!

    • Paola says:

      Hi Michelle! OK, so full disclosure is that I don’t own a microwave so I’ve never mad a mug cake 🙊

      Having said that, you guys keep asking for it so I’ll work on it! And on these muffins, I’m also solo and I freeze EVERYTHING! Shocker is that keto baked goods tend to freeze great (things like cookies and brownies are awesome even frozen… ooops!). I hope this helped xo!

      • Michelle says:

        Good to know they freeze well! I actually started the filling, put into a mini ice mold and I was able to drop one in my coffee today! 😉 So yummy! I only recently have made the microwave mug cakes myself. They are easy at work. shh

        Once again, thank you for all the wonderful recipes!

  7. April says:

    5 stars
    Hi! These were great, however, my tops do not look like yours! The batter was very thick and it stayed in the shape I put them in the cupcake tin. They were also dry.
    I’m not sure what’s I’m going wrong, but I hope to try them again! Any suggestions?

  8. Jorge says:

    5 stars
    Pumpkin recipes are what I freakin live for. I love this tine of the year. This recipe looks great and I can’t wait to give it go pretty soon. thank you!

  9. Wendy Ellis says:

    I’m not a coffee fan, but I LOVE chai tea and it goes so well with pumpkin and spice flavors. Is there a way to use some super-concentrated form of brewed chai in this recipe instead?

  10. Christy Cyr says:

    5 stars
    I would dearly love a pumpkin bread recipe! Just sayin’ … fall is coming up in the northern hemisphere. 😉 This muffins look so delicious, but I’ve had failure after failure trying to make a pumpkin bread on my own.

    By the way, these muffins were fantastic!

  11. June says:

    5 stars
    Made a double batch of these (with cream cheese and streusel, sans frosting) and they are sooo yummy!

    For anyone wondering, I froze some and they held up beautifully when defrosted! 🙂

  12. Amira says:

    These look wonderful and am so excited to try them! I was just wondering if there is a possible substitution for the cream cheese in the pumpkin filling, as not everyone in the house is doing Keto with dairy.

    • Paola says:

      Thank you Amira! In all honesty I haven’t tried with anything else myself, but I do remember form last year that one reader made them with vegan cream cheese (I hope this helps!) xo

    • Paola says:

      Hi Marjorie! I don’t see why not! Just watch out as they’ll probably be done a bit quicker in a donut pan xo!

  13. Vanessa says:

    Hi! Everything smells amazing. They are still baking. Quick question- am I supposed to use the egg whites in the recipe too? The batter was very dry- almost like a cookie dough.

    • Paola says:

      Hi Vanessa! Yes the egg whites should have been beaten until soft peaks form and folded in at the end. I have now added it as an extra step as it was lumped together in the previous one and maybe easy to miss. Hopefully still turn out relatively OK?

      xo! Paola

  14. Reader says:

    5 stars
    I never leave comments, but I had to for these, because how on earth are these legal?! I mean BEST MUFFIN RECIPE I’VE EVER MADE! KETO OR NOT OR WHATEVER! Now I get all the caps going about!!

    PEOPLE MAKE THIS RECIPE TO THE LETTER! OK so maybe I did use instant coffee as I don’t have an espresso machine… but still! Truly out of this world!

  15. Trisha says:

    Sadly these sound wonderful but I’m one of the few it seems that doesn’t like coffee is there another liquid you think would work?

    • Paola says:

      Hi Trisha! Well given that the coffee doesn’t do much more other than impart flavor, you could just sub in with water and add in a touch more pumpkin spice or vanilla? xo! Paola

  16. dianars says:

    5 stars
    I just made these and I must say they’re AMAZING! First keto thing I bake that I actually LOVE!

    I have one suggestion, that you always double the batch 😉

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