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Home/Low Carb Recipes/Keto Pumpkin Muffins With Cream Cheese
Freshly baked keto pumpkin muffins topped with cream cheese frosting on a wooden table.
Low Carb Recipes

Keto Pumpkin Muffins With Cream Cheese

By Adam John
July 5, 2026 2 Min Read
0

This post contains affiliate links. As an Amazon Associate, I earn from qualifying purchases. This comes at no extra cost to you.

Keto fall baking recipes bring the perfect combination of moist pumpkin muffins and creamy filling into one irresistible bite. These Keto Pumpkin Muffins With Cream Cheese are made with almond flour, coconut flour, unsweetened pumpkin puree, and a sweet cream cheese center. Ready in under 35 minutes, they deliver a satisfying low-carb treat with the flavors of fall. During my busy coaching days, quick keto-friendly snacks like these muffins keep me fueled without compromising my goals, making them a lifesaver in my routine.

Table of Contents

  • Why Make Keto Pumpkin Muffins With Cream Cheese?
  • What Ingredients Do You Need for Keto Pumpkin Muffins With Cream Cheese?
  • How Do You Make Keto Pumpkin Muffins With Cream Cheese Step by Step?
  • Frequently Asked Questions About Keto Pumpkin Muffins With Cream Cheese
  • What Should You Serve with Keto Pumpkin Muffins With Cream Cheese?
  • Common Mistakes to Avoid When Making Keto Pumpkin Muffins
  • How to Store and Reheat Keto Pumpkin Muffins With Cream Cheese

Why Make Keto Pumpkin Muffins With Cream Cheese?

Keto Pumpkin Muffins With Cream Cheese make a flavorful, low-carb snack or breakfast option with the rich taste of pumpkin and a creamy filling. They offer keto-friendly nutrition while indulging your fall cravings.

  • The spicy blend of cinnamon, nutmeg, and ginger pairs perfectly with pumpkin, creating a quintessential autumn treat.
  • Made with almond and coconut flour, these muffins are gluten-free and keto-compliant, fitting seamlessly into your dietary lifestyle.
  • With simple ingredients and just 35 minutes, you can whip these up even during a hectic day.
  • Whether for breakfast or a quick pick-me-up, these muffins satisfy hunger without sacrificing health goals.

What Ingredients Do You Need for Keto Pumpkin Muffins With Cream Cheese?

This recipe calls for essential low-carb ingredients, including almond flour, canned pumpkin puree, and a keto-friendly sweetener. Each component creates the texture and flavor that make these muffins special.

  • 1 cup almond flour
  • 1/4 cup coconut flour
  • 1/3 cup granulated erythritol (or preferred keto sweetener)
  • 1 tsp baking powder
  • 1/2 tsp baking soda
  • 1/2 tsp ground cinnamon
  • 1/4 tsp ground nutmeg
  • 1/4 tsp ground ginger
  • 1/4 tsp salt
  • 3 large eggs
  • 1/2 cup canned pumpkin puree (unsweetened)
  • 1/4 cup unsalted butter, melted
  • 1 tsp vanilla extract
  • 4 oz cream cheese, softened
  • 1 tbsp erythritol (for cream cheese filling)
  • 1/2 tsp vanilla extract (for cream cheese filling)

Almond flour provides a sturdy base that keeps the texture moist yet light, while erythritol sweetens without spiking blood sugar levels.

How Do You Make Keto Pumpkin Muffins With Cream Cheese Step by Step?

This recipe involves simple mixing and layering to create perfectly moist muffins with a rich cream cheese center. Here’s how to make them:

Step 1 — Preheat the Oven

Preheat your oven to 350°F (175°C) and line a muffin tin with paper liners or grease it well with non-stick spray.

Step 2 — Mix Dry Ingredients

In a large mixing bowl, whisk together almond flour, coconut flour, erythritol, baking powder, baking soda, cinnamon, nutmeg, ginger, and salt.

Step 3 — Combine Wet Ingredients

In a separate bowl, combine eggs, pumpkin puree, melted butter, and vanilla extract. Mix until smooth.

Step 4 — Combine Mixtures

Gradually add the wet ingredients to the dry ingredients, stirring until fully combined and a thick batter forms.

Step 5 — Prepare Cream Cheese Filling

Mix softened cream cheese, erythritol, and vanilla extract in a small bowl until smooth.

Step 6 — Assemble Muffins

Spoon 2 tablespoons of batter into each muffin cup, filling halfway. Add a teaspoon of cream cheese filling to the center, then top with more batter to cover the filling.

Step 7 — Bake

Bake for 20-25 minutes until muffins are set and a toothpick (avoiding the cream cheese center) comes out clean.

Step 8 — Cool and Serve

Cool muffins in the pan for 10 minutes, then transfer to a wire rack to finish cooling completely.

Freshly baked keto pumpkin muffins topped with cream cheese frosting on a wooden table.
Jump to Recipe Print Recipe

Frequently Asked Questions About Keto Pumpkin Muffins With Cream Cheese

Can I use a different sugar substitute?

Yes, you can swap erythritol for Monkfruit or Stevia-based sweeteners, but be mindful of equivalencies.

KitchenAid Artisan Stand Mixer

Kitchen ApplianceKitchenAid Artisan Stand Mixer

Makes mixing batters and cream cheese fillings effortless — a kitchen game-changer.

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Wilton Non-Stick Muffin Pan 12-Cup

Essential CookwareWilton Non-Stick Muffin Pan 12-Cup

Essential for baking perfectly shaped muffins — durable and easy to clean.

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How can I ensure my cream cheese filling stays creamy?

Use softened cream cheese and beat it thoroughly with erythritol and vanilla extract for a smooth texture.

Are these muffins gluten-free?

Absolutely! Using almond and coconut flour makes them completely gluten-free.

Can I freeze these muffins?

Yes, store cooled muffins in an airtight container and freeze for up to one month.

What’s the best way to reheat frozen muffins?

Thaw them at room temperature and warm in the oven at 300°F for 5-7 minutes.

What Should You Serve with Keto Pumpkin Muffins With Cream Cheese?

Pair these muffins with:

  • Our cold stuffed mini peppers for a savory complement.
  • A cup of black coffee or herbal tea for a comforting balance.
  • Fresh berries to enhance the sweetness naturally.

Common Mistakes to Avoid When Making Keto Pumpkin Muffins

Avoid these pitfalls:

  • Overmixing the batter can make muffins dense instead of moist. Stir until just combined.
  • Using cold cream cheese can result in a chunky filling. Ensure it’s softened before mixing.
  • Skipping the cooling step may cause the muffins to fall apart. Let them cool completely before serving.

How to Store and Reheat Keto Pumpkin Muffins With Cream Cheese

Store leftovers in an airtight container in the fridge for up to 5 days. For longer storage, wrap tightly and freeze for up to one month. Thaw frozen muffins at room temperature before reheating at 300°F for 5-7 minutes.

Freshly baked keto pumpkin muffins topped with cream cheese frosting on a wooden table.

Keto Pumpkin Muffins With Cream Cheese

Delicious keto-friendly pumpkin muffins with a creamy center, perfect for fall or any time of year.
Print Recipe Pin Recipe
Prep Time 15 minutes mins
Cook Time 25 minutes mins
Total Time 40 minutes mins
Servings: 12 muffins
Course: Dessert, Snack
Cuisine: American
Calories: 150
Ingredients Equipment Method Notes

Ingredients
  

  • 1 cup almond flour
  • 1/4 cup coconut flour
  • 1/3 cup granulated erythritol or preferred keto sweetener
  • 1 tsp baking powder
  • 1/2 tsp baking soda
  • 1/2 tsp ground cinnamon
  • 1/4 tsp ground nutmeg
  • 1/4 tsp ground ginger
  • 1/4 tsp salt
  • 3 large eggs
  • 1/2 cup canned pumpkin puree unsweetened
  • 1/4 cup unsalted butter melted
  • 1 tsp vanilla extract
  • 4 oz cream cheese softened
  • 1 tbsp erythritol for cream cheese filling
  • 1/2 tsp vanilla extract for cream cheese filling

Equipment

  • mixing bowl
  • whisk
  • muffin tin
  • oven
  • wire rack

Method
 

  1. Preheat your oven to 350°F (175°C) and line a muffin tin with paper liners or grease well with non-stick spray.
  2. In a large mixing bowl, whisk together almond flour, coconut flour, erythritol, baking powder, baking soda, cinnamon, nutmeg, ginger, and salt.
  3. In a separate bowl, combine eggs, pumpkin puree, melted butter, and vanilla extract. Mix until smooth.
  4. Gradually add the wet ingredients to the dry ingredients, stirring until fully combined and a thick batter forms.
  5. In a small bowl, prepare the cream cheese filling by mixing softened cream cheese, erythritol, and vanilla extract until smooth and creamy.
  6. Spoon about 2 tablespoons of the muffin batter into each prepared muffin cup, filling them halfway.
  7. Add a small dollop (about 1 teaspoon) of the cream cheese filling to the center of each muffin cup.
  8. Top each muffin with another spoonful of batter to cover the cream cheese filling, filling the cups about 3/4 full.
  9. Bake in the preheated oven for 20-25 minutes, or until the tops are set and a toothpick inserted into the muffin (avoiding the cream cheese center) comes out clean.
  10. Allow the muffins to cool in the pan for 10 minutes, then transfer them to a wire rack to cool completely.

Notes

For best results, use room-temperature cream cheese for the filling. Store leftovers in an airtight container in the refrigerator for up to 5 days.
Freshly baked keto pumpkin muffins topped with cream cheese frosting on a wooden table.

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Author

Adam John

Adam John is a Nutrition Expert based in Florida with more than 20 years of experience in nutrition. His work began with one question: why do so many people suffer from illnesses that diet and lifestyle can help prevent? At XNutrion, Adam writes about vitamins, minerals, supplements, and healthy eating, and he reviews our supplement and weight loss content before it is published.

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