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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. Soobie Doobie says:

    Hi! I was wondering how you fill the middle of the muffin? I scoop the batter into the muffin tin, then I use a spoon to push the the batter and make a “hole” in the middle, and then fill it with the cream cheese filling. But when I bake it the muffin “collapses” and it’s like it’s hollow, as if the cream cheese filling got absorbed into the batter? Flavour is still amazing, but would love any tips on how to make the middle of my muffins look luscious and full of cream cheese like yours. Thanks!

  2. Dawn says:

    I cannot wait to try these however something happened with my cupcakes in the oven, they sunk in the middle. Also I noticed they were very very large for only six cupcakes I actually could have made 12. My Tinsley no smaller than any other cupcake 10. I’m wondering why the cupcakes sunk though in the middle?

  3. scott gilmore says:

    I just moved to a more relaxed keto diet after 3 years. I found your site and these were great. My wife said I have been baking good stuff but this was truly the first thing she would call great. It did take time but they came out excellent. I don’t do caffeine so left the coffee out and dont think it hurt the receipe one bit. The issue I had was getting the thin layer on top of the cream cheese. But I will definitely make them again. Thank you.

  4. Clare Hintz says:

    5 stars
    I love these muffins! Plenty sweet for my tastes and the coffee adds a nice earthy note. Makes a great alternative to pumpkin pie. So moist and fluffy… thanks for including the sour cream alternative! I have to stay away from dairy too, so these options are helpful. I’m still messing around with cream cheese alternatives. I use a frosting made with ghee instead of the buttercream. I freeze cooked pumpkin from the garden in small quantities to have these muffins all winter.

  5. Lisa says:

    5 stars
    I am so late to the PSL craze because I was never one to drink coffee. Now that I can enjoy it with heavy cream I’m all in 👍 Pumpkin spice frappes are my morning drink of choice lately. Soon to be followed by the Gnom-Gnom hot chocolates as the weather cools. I know I will enjoy these PSL cupcakes! Thanks Paola 🤗🥰

  6. Jeanette says:

    5 stars
    These took a long time but were delicious! I didn’t make the streusel and added extra coffee! I think if you use good coffee these will come out well. I tried to freeze the filling but it wasn’t completely frozen but still turned out great!

  7. Angelina says:

    5 stars
    In the oven now! They smell like autumn. A lot of work but I then know it’s well worth it. Do yourself a favor and double the recipe so you can have 12 muffins. Even hubby had a lick of the batter and loved it.

  8. Katie says:

    Before low carb I used to make a very simple muffin with pumpkin puree and spice cake mix. Looking for a compromise so I’ll try this to base my work upon. You should see what I did with banana bread!

  9. Marla says:

    The look of them made me want to try them (they are very pretty!) but I was disappointed. Really disappointed. It was a LOT of work for something that ended up having no taste. Too many ingredients fought each other. Too complex and not user friendly for this baker.

    • Paola says:

      Hi Maria! Folding in egg whites etc is a bit more advanced baking so something could’ve gone wrong. Regarding the no taste, could it be that you thought they needed more sugar? (keto palates vary A LOT!). xo!

      • Marla says:

        I did an awesome job folding in the egg whites Paola! I liked the recipe because it was a challenge, and yes maybe it needed more sweetness. I used the Monkfruit golden and classic, and when tasting the batter it seemed to be fine. I think my problem was the coffee fought the pumpkin spice flavor. I agree Keto palates do vary a lot. I’ve been Keto for 15 months and have enjoyed the relearning how to bake. I think I learned my lesson here however, for me, Keep it Simple! LOL!

        • Paola says:

          I’m not saying you didn’t fold the egg whites properly (how could I know?! 😂). I’m just saying that yes, recipes which involve you whipping egg whites etc do require more baking skill (which you only get by attempting these sort of recipes… catch 22?!) xo!

  10. Mp says:

    5 stars
    This recipe looks fabulous – can’t wait to try it!!! But I actually don’t like the taste of coffee – any suggestion on what I can replace the espresso or coffee with? Almond milk? Coconut milk?
    I don’t want to Loose the moisture or texture
    But love pumpkin spice!!!

  11. Reba Hamilton says:

    I am about to make these. I printed the recipe with Metric but then noticed my mistake and just now wrote down the converted measurements. One confusion, though. When I use the conversion, the streusel topping does not make sense. In metric it says 64g almond flour and 21g coconut flour which is the same as the muffin recipe. But when converted, it says the muffins have 2/3 C almond and 3T coconut but the same numbers in streusel convert to 1/3C almond and 4T coconut. Which is correct? The metric measurement or the US measurement?

  12. Jackie says:

    I was very excited to make these! I followed the recipe to a T! The batter was very thick and had more of a cookie dough consistency. I did the frozen filling ahead of time. These took FOREVER to bake and did not taste very good. Very bummed out 😔

    • Paola says:

      Oh no Jackie! Do note that the consistency is VERY thick (yup cookie dough like!), so did you add more liquid to thin it out? Because that would’ve accounted for the longer baking time etc. Alternatively, if you didn’t like the taste what sweetener did you use? xo!

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