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    Home » Dessert

    Keto Pumpkin Muffins with Almond Flour

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    Modified: Sep 8, 2026 · Published: Oct 6, 2021 by Wendy Polisi · 1 Comment

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    For coffee shop vibes without the sugar crash, nothing beats these keto pumpkin muffins. Made with almond flour and whey protein, they are a fall treat that's hearty enough for breakfast. With a tender crumb and rich pumpkin flavor, it is a keto muffin you will turn to all season long.

    Pumpkin muffins topped with chopped pecans are stacked on a wooden board, with autumn decorations like pumpkins and pinecones in the background. One muffin has a bite taken out, showing its moist interior.

    I published a pumpkin muffin recipe on the site.  And it was good.  But not so good that I found myself dreaming of it on September 1.  I had this nagging feeling that I could do better, so I went back to the kitchen and started fiddling.

    This keto pumpkin muffin recipe is what came out the other side.  I knew I had it right when my daughter declared it a good muffin. Not just “good for keto”.  That does-not-feel-low-carb thing is what I was chasing.

    I know the ingredient list is a little long, but every single thing is there for a reason.  I’ll explain why each of them helps make the perfect low-carb pumpkin muffin.

    As an amazon associate, I earn from qualified sales.

    Baking ingredients on a marble counter for delicious pumpkin keto muffins: a yellow bowl with dry ingredients, a blue bowl with three eggs, a stick of butter, a cup of pumpkin puree, small cups of milk, vanilla, and a small bottle of food coloring—everything you need to start your favorite keto pumpkin muffins recipe.

    Let's Talk Ingredients

    The lift in these almond flour pumpkin muffins comes mostly from the unflavored whey protein isolate.  It sounds like a gym-bag thing, I know.

    But in keto baking, it helps to build structure in the same way gluten does in a wheat muffin.  It is what gets you that tender crumb.

    The almond flour brings moisture, fat, and richness. This is the brand I use, because it is the least expensive one that works that I've found.  We add in a little coconut flour to soak up liquid so the batter isn’t too loose.

    Make sure you let your eggs come to room temperature first. If you forget to pull them out like I do, let them soak in a bowl of warm (but not too hot) water for about 15 minutes.

    Oat fiber is a little bit of a specialty ingredient. Don't sweat it if you don't have it. It isn't necessary for the structure; it just adds a little lightness.

    The xanthan gum keeps the muffins from being too crumbly. Don’t use more than it calls for because things can get gummy quickly.

    Make sure you use pure pumpkin and not pumpkin pie filling.

    I tested this with several sweeteners, and preferred the results with monkfruit allulose blend.  Allulose alone made the muffins too soft and not sweet enough.  Swerve left a cooling aftertaste that I'm not a fan of. (But feel free to use it if it doesn't bother you.)

    Tips for the Best Consistency

    • Aim for a batter that's thick but soft. It shouldn't hold its shape like an ice cream scoop, but you shouldn't be able to pour it either.
    • Pumpkin's water content varies by brand. If the batter looks too dry, add a tablespoon or two of almond milk or heavy cream.
    • Don't skip the five-minute rest before scooping. It is necessary for the coconut flour to absorb the liquid.
    • This batter does not self-level in the oven. You can use a wet fingertip to smooth the tops.

    Why We Change the Oven Temp

    The high-heat start makes the muffins rise and gives them a rounded top. If we kept the temperature high the entire time, the tops would burn before the center is done.

    Judging Doneness

    As soon as a toothpick comes out clean, they are done.  Whey protein firms as it cools. When testing I discovered that the muffins that looked perfect straight from the oven were overcooked when they cooled.

    About the Molasses

    I want to explain the molasses, because it's fair to wonder why it's hanging out in a keto recipe.

    Molasses gives a flavor that keto brown sugar doesn't quite get.

    One teaspoon spread across the whole batch is a small amount. Still, molasses is sugar. If it doesn't fit the way you eat, leave it out.

    What to bake next

    My keto pumpkin bread is another fall favorite.  When you want a muffin in the rotation on a regular week, my almond flour protein muffins are perfect.

    How to Make Keto Pumpkin Muffins

    A yellow bowl with a metal whisk mixing brownish dry ingredients for keto pumpkin muffins sits on a marble countertop.
    Mix together the dry ingredients.
    An orange mixing bowl with a small amount of light brown batter or sauce at the bottom, placed on a gray marble countertop—perfect for preparing your favorite keto pumpkin muffins recipe.
    Mix the wet ingredients in another bowl.
    A red mixing bowl with brown cookie dough for keto pumpkin muffins and a black spatula sits on a marble countertop.
    Add the dry ingredients to the wet ingredients. Let the batter sit for 5 minutes to hydrate.
    A muffin tin lined with paper cups, each filled with unbaked brown batter for keto pumpkin muffins, sits on a light marble countertop.
    Scoop and top with nuts if you like. Bake, cool, and enjoy!

    You can frost keto pumpkin muffins with Cream Cheese Frosting for a cupcake effect.

    Three pumpkin muffins in black wrappers are stacked on a wooden tray, topped with chopped nuts. A pumpkin, pine cone, and white fabric are in the background, creating an autumnal scene.
    If you like this recipe don't forget to leave a 5 star rating and let me know how it went in the below comments, I love hearing from you! You can also FOLLOW ME on FACEBOOK, INSTAGRAM, and PINTEREST to see all my delicious recipes.
    Three pumpkin muffins in black wrappers are stacked on a wooden surface, topped with chopped nuts. A pinecone and a pumpkin are visible in the background.
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    Keto Pumpkin Muffins with Almond Flour

    For coffee shop vibes without the sugar crash, nothing beats these keto pumpkin muffins. Made with almond flour and whey protein, they are a fall treat that's hearty enough for breakfast. With a tender crumb and rich pumpkin flavor, it is a keto muffin you will turn to all season long.
    Prep Time15 minutes mins
    Course: Dessert, Snack
    Cuisine: American
    Diet: Gluten Free, Vegetarian
    Keyword: keto muffins, pumpkin
    Servings: 12
    Calories: 193.73kcal
    Author: Wendy Polisi
    As an Amazon Associate I earn from qualified sales.
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    Ingredients

    Dry

    • 210 grams blanched super-fine almond flour 1 ¾ cups + 2 tablespoons
    • 2 tablespoons unflavored whey protein isolate
    • 2 tablespoons coconut flour
    • 2 tablespoons oat fiber optional; adds lightness
    • ⅔ cup powdered monk fruit allulose blend
    • 2 teaspoons baking powder aluminum-free
    • ¼ teaspoon baking soda
    • ¼ teaspoon xanthan gum
    • 2½ teaspoons pumpkin pie spice
    • ½ teaspoon sea salt

    Wet

    • 3 large eggs room temperature
    • 1 cup pumpkin purée melted and slightly cooled
    • ⅓ cup butter
    • 2 tablespoons heavy cream
    • 1 teaspoon molasses optional ingredient; omit for strict keto
    • 2 teaspoons vanilla extract

    Instructions

    • Preheat your oven to 375°F. Line a muffin tin.
    • In a medium bowl, whisk together the almond flour, whey protein, coconut flour, oat fiber, sweetener, baking powder, baking soda, xanthan gum, pumpkin pie spice, and sea salt.
    • In a large bowl, beat together the eggs, pumpkin puree, heavy cream, molasses (optional), and vanilla.
    • Add the dry ingredients to the wet ingredients and stir until just combined. Let the batter rest for 5 minutes.
    • Scoop into the prepared muffin pan. Wet a finger, then smooth each top. Sprinkle with nuts or keto chocolate chips if desired.
    • Bake for 6 minutes. Without opening the oven door, reduce the temperature to 350 °F. Bake for 14 to 18 minutes more, until a toothpick comes out clean and the tops spring back.
    • Cool in the pan for 15 minutes, then move to a rack to cool completely.

    Notes

    Storing and freezing
    Store leftovers in an airtight container in the fridge for 5 days. I always put them in the microwave for 15 seconds to soften the crumb.
    I usually freeze at least half of them right away. To do this, cool them, and then place them in a single layer in a freezer bag. They will keep for 3 months.
    A frozen muffin thaws on the counter in about an hour, or twenty-five seconds in the microwave for the mornings you can't wait.

    Nutrition

    Calories: 193.73kcal | Carbohydrates: 7.49g | Protein: 7.58g | Fat: 16.16g | Saturated Fat: 5.03g | Polyunsaturated Fat: 0.45g | Monounsaturated Fat: 1.97g | Trans Fat: 0.21g | Cholesterol: 61.19mg | Sodium: 186.2mg | Potassium: 139.43mg | Fiber: 3.73g | Sugar: 1.76g | Vitamin A: 3438.48IU | Vitamin C: 0.97mg | Calcium: 90.86mg | Iron: 1.47mg
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    About Wendy Polisi

    Wendy Polisi is a recipe developer, food photographer, and author of five cookbooks, including The Easy Low Carb Cookbook and The Ultimate Keto Air Fryer Cookbook. As a single mom of three, she knows dinner has to be fast, real, and satisfying. On Kicking Carbs, she shares low-carb and keto recipes made from scratch. Comfort food that fits your goals without tasting like a compromise.

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    1. Rita says

      December 20, 2020 at 7:53 pm

      Are there any good substitutes for oat fibre?

      Reply
    A smiling woman in a white shirt stands at a kitchen counter outdoors, slicing lemons. There is a pitcher of lemonade, two glasses, and a plant on the table. Behind her are potted plants and gardening tools hanging on the wall.

    Welcome!

    I'm Wendy and I'm here to show you just how delicious a low carb, gluten free and keto diet can be! You are just as likely to find me obsessing over all things cheesy as you are getting excited by a full produce drawer. I'm a mom to three, obsessive planner and roller coasters are my happy place.

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    Welcome to the Kicking Carbs website (“site“). Wendy Polisi is not a health professional and information on this blog, arising from this blog, or social media related to this blog is only her personal experience and opinions. You should always check with your health care provider before beginning any diet, health plan, or lifestyle change.

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