Pumpkin Pecan Muffins (Gluten-Free)

A plate of muffins on a table

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Well, it’s officially fall. And fall is the season of pumpkin everything. I’m joining right in with these Pumpkin Pecan Muffins. I made these muffins with almond flour and they are a delicious way to enjoy pumpkin, one of the food stars of autumn.

Pumpkin Pecan Muffins in a muffin pan

Almond Flour, or Almond Meal, Are They the Same?

Although both almond flour and almond meal are made from ground almonds, they are not the same. For almond flour, the almonds are blanched and peeled before grinding very finely. Almond flour is lighter in colour and finer than almond meal, making it a good alternative to all-purpose flour in baked goods.

Almond meal is made from raw almonds and includes the skin, giving it a coarser texture and a darker colour. I love almond meal as a breading ingredient for chicken or shrimp, and it works well in homemade granola and energy balls. 

A pan of Pumpkin muffins

Can I Substitute All-Purpose Flour in This Recipe?

The answer is yes, you can substitute all-purpose flour for the almond flour. This is possible because almond flour is a 1.1 measure for measure in recipes with all-purpose flour. However, without the texture and flavour of the almond flour, these won’t be the same muffin. If possible, I really encourage you to give the almond flour a try. Even if gluten isn’t an issue for you, almond flour adds a delicious twist to many baked goods. A couple of delicious examples: Apple Ricotta Cake or Cranberry Date Squares

Two pumpkin pecan muffins on a white plate

Can I Substitute Any Other Flour for Almond Flour?

There are lots of alternative flours. Some common ones are coconut flour, chickpea flour, oat flour, buckwheat flour, as well as other nut flours. None of them can be used in this recipe without a lot of tinkering and no guarantee of success. Each specific flour has a different weight, and different levels of fat, protein and carbohydrates. And each type of flour absorbs moisture differently, requiring the addition of more or less liquid, oil, or eggs. 

Muffins on a plate on a table

Canned Pumpkin Puree VS Fresh 

Fresh everything is always better tasting, in my books. However, sometimes convenience has to win, and canned pumpkin puree is convenient, tasty and nutritious. I used canned pure pumpkin puree for these muffins. You can use fresh pumpkin flesh to make this recipe, but you will need to cook and puree it first. If you want to see a comparison, this is a great article: Canned Pumpkin vs Fresh Pumpkin.

A table topped with muffins on plates

Pumpkin: It’s Very Nutritious

Every fall, it’s fun to see how much people love to jump on pumpkin recipes and embrace pumpkin spice everything. Which is so great, because pumpkin is actually not just tasty, but also crazy, super healthy. Both canned and fresh pumpkin are loaded with nutrients, including Vitamin A, C, E and minerals Potassium, Magnesium and Iron. And additionally, pumpkin is loaded with fibre and antioxidants, too. 

Pumpkin Pecan Muffins on a white platter

Are These Muffins Healthy?

Pumpkin, as I mentioned, is highly nutritious. Almonds and pecans, like most nuts, are high in fibre and hearty healthy fats. Nuts, as well as eggs are also protein-rich, so these pumpkin pecan muffins are perfect for breakfast or snacks and will keep you full for a long time. 

A Pumpkin muffins on a plate

Versatile Pumpkin: For Sweet or Savoury Recipes

Guess what? Pumpkin is more than just pie. Try it in recipes like:

Pumpkin Spice Loaf

Roasted Pumpkin Hummus

Jamaican Pumpkin Soup

A half-empty pan of muffins on a table


A plate of muffins on a table

Pumpkin Pecan Muffins

Almond flour and pecans make these healthy pumpkin muffins protein-packed and gluten-free as well as delicious.
5 from 21 votes
Prep Time 10 mins
Cook Time 20 mins
Total Time 30 mins
Course Quick Breads & Muffins
Cuisine American, Canadian
Servings 12 muffins
Calories 250 kcal


  • 1 3/4 cups almond flour
  • 1/2 cup dark brown sugar
  • 2 tsp baking powder
  • 1 tsp ground ginger
  • 1 tsp cinnamon
  • 1/2 tsp baking soda
  • 1/2 tsp salt
  • 1/4 tsp ground cloves
  • 1/4 tsp nutmeg
  • 1 cup chopped pecans
  • 2 large eggs beaten
  • 1 cup pumpkin puree
  • 1/4 cup vegetable oil
  • 1 tsp vanilla extract


  • Preheat oven to 350°
  • Line a 12 cup muffin pan with paper liners or spray with cooking spray
  • In a large bowl, whisk together almond flour, sugar, baking powder, ginger, cinnamon, baking soda, salt, cloves, nutmeg, and half of the pecans
  • In another bowl, whisk together eggs, pumpkin puree, vegetable oil and vanilla
  • Stir the pumpkin mixture swiftly into the dry ingredients, mixing until just combined
  • Spoon into the prepared muffin cups, dividing evenly.
  • Sprinkle tops with the remaining pecans
  • Bake in the centre of the oven until the tops are golden and firm to the touch. (About 20 minutes)
  • Cool in the pan on a rack for 5 minutes
  • Remove muffins from the pan and allow to cool completely on a rack.


Walnuts or slivered almonds can be easily substituted for the pecans.
Dark brown sugar adds a nice caramelized flavour, but light brown sugar, or coconut sugar work as well. 
Store muffins in an airtight container at room temperature for up to two days.
To freeze baked muffins, allow to cool completely, then flash freeze the muffins on a tray until solid, about 30 minutes. Pack into an airtight freezer-safe container. 
To freeze muffin batter, after filling the muffin cups, place the pan in the freezer for about 4 hours or until frozen solid. Pack into an airtight freezer-safe container. When you're ready to bake, remove the number of muffins that you need and put them in a muffin pan. Bake in a preheated oven 25-30 minutes.
If you are freezing muffin batter, its a good idea to label the container or bag with the baking temperature and time. 


Serving: 1muffinCalories: 250kcalCarbohydrates: 16gProtein: 5gFat: 20gSaturated Fat: 5gCholesterol: 27mgSodium: 164mgPotassium: 186mgFiber: 3gSugar: 11gVitamin A: 3222IUVitamin C: 1mgCalcium: 96mgIron: 1mg
Keyword almond flour, fall, pecans, pumpkin puree
Tried this recipe? What changes did you make?Let us know how it was!



39 thoughts on “Pumpkin Pecan Muffins (Gluten-Free)

  1. I love the texture of these muffins! Almond flour adds so much interest and even flavour! Thanks for a great recipe!

  2. I’m right there with everyone in the ‘pumpkin everything’ camp as soon as I notice the leaves changing. And these look perfect for fall- especially love that they are healthy too! Thanks for explaining the difference between almond flour and almond meal – I always wondered!

  3. I wanted to bake our neighbor something special but she can’t eat things flour — she has trouble digesting them. Well, I made her these pumpkin pecan muffins and her whole family loved them. She liked them so well she asked for the recipe — I guess there will be two of us making this recipe regularly.

  4. Pecans and pumpkin go so well together! We made these last night and they disappeared so fast! They were just perfect with our afternoon tea!

  5. Such perfect timing – I’ve got a lot of extra pumpkin (well, red kuri squash, but same idea) puree in the fridge right now and I’m looking for things to make with it. These are delightful, and I love the use of pecans. It’s a perfect flavour pairing with pumpkin and squash!

  6. Me and my munchkins made these for breakfast this morning. We froze half for next week and loved enjoying the fruits of our labor.

  7. Mmmmm … what a delicious idea to use almond flour in this recipe! Even though I’m not gluten-sensitive, I love the idea of subbing nutritious (and yummy!) almond flour to really build the nutty notes in these muffins, along with those crunchy pecans!

  8. Great looking muffins. I especially love the crunchy texture on top and the fact they are gluten free. There’s a pumpkin option for everyone!

  9. I was looking for a gluten-free Pumpkin muffin recipe and this recipe was perfect! I loved the flavor and how moist they were! Definitely making these again for the holidays.

  10. These muffins are delicious and so perfect for the fall! They came out super moist, and the spice level was just right. Definitely worth making again during these fall months!

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