Pumpkin Gingerbread Muffins with Lemon Glaze

Pumpkin Desserts & Baked Goods

Pumpkin gingerbread muffins with lemon glaze are gluten free, dairy free, and naturally sweetened — the perfect muffins for the holiday season! They are packed with pumpkin, warm spices and molasses for that gingerbread taste!

fluffy, moist and delicious gluten and dairy free pumpkin gingerbread muffins with fresh orange zest
In this batch of muffins, I used regular molasses, not blackstrap which is why they are lighter in color.

If you’re like me and not quite ready to give up on pumpkin after Halloween or Thanksgiving, whip up a batch of these healthy pumpkin gingerbread muffins made with simple ingredients in December! Molasses and ginger give them extra holiday flavor and that classic gingerbread taste. I say pumpkin season is truly year-round!

Made gluten and dairy free with a blend of almond and oat flour, these healthy pumpkin gingerbread muffins will hit the spot alongside a cup of coffee on a chilly December morning. The citrus glaze is totally optional, but it definitely adds a little extra flavor and bright sweetness.

Pumpkin Gingerbread Muffins

Pumpkin puree, pumpkin spice, ginger and molasses come together for a perfectly spiced muffin that marries the flavors of fall and winter! The blend of almond and oat flour in this recipe give the muffins an extra fluffy and soft texture that I know you’ll love as much as I do!

One tip to keep in mind when you’re baking any type of muffins is to not over mix the batter. The batter should be mixed together just so and you should still see some lumps. At that point you can start portioning out the batter into the individual muffin tins.

best pumpkin gingerbread muffins

Nutrition Benefits of Pumpkin Puree

Pumpkin puree is a great source of a lot of vitamins and minerals which is one of the many reasons I love cooking and baking with it all fall long! It’s super versatile, adding flavor and texture to both sweet and savory foods — not many other fruits and vegetables can say the same.

Maybe you’ve noticed that a lot of gingerbread flavored treats contain molasses, but what is molasses and is it good for you? Let’s find out!

healthy gingerbread muffins

What is Molasses and is it Healthy?

Blackstrap molasses is a byproduct of sugar cane’s refining process. Sugar cane is mashed to create juice, and then boiled once to create cane syrup. A second boiling creates molasses.

Blackstrap molasses has the lowest sugar content of any sugar cane product and is actually packed with vitamins and minerals like iron, calcium, magnesium, B6 and selenium. It’s also digested slower than other sweeteners, which is good for blood sugar balance. Known for giving gingerbread its distinctive taste, you can use it in other ways too like a glaze for chicken!

almond flour gingerbread muffins

Ingredients for almond flour gingerbread muffins

Here’s everything you will need to make these pumpkin gingerbread muffins with lemon glaze!

  • blanched almond flour
  • oat flour (gluten free if preferred)whole-wheat pastry flour can be substituted for oat flour. Note, whole-wheat pastry flour is not gluten free.
  • blackstrap molassesmolasses is what gives these muffins that gingerbread flavor. You can definitely use regular molasses vs. blackstrap. Your muffins will come out lighter in color when using regular molasses.
  • pumpkin pureeas with any of my pumpkin recipes, be sure to use pumpkin puree and not pumpkin pie filling! I love using Libby’s 100% Pure Pumpkin in all of my pumpkin recipes.
  • maple syrup
  • unsweetened almond milk or other milk of choice
  • pumpkin pie spice
  • lemon juice
  • lemon zest or orange zest
  • coconut oil
  • baking soda
  • confectioners sugar

equipment / utensils needed:

How to Make The Glaze

Making the lemony glaze for these gluten free gingerbread muffins is super easy! All you need to do is mix together the confectioners sugar, maple syrup, lemon juice, and vanilla extract.

You want the consistency to be thin enough to drizzle on top of each muffin. If your icing is too thick add a little more almond milk, if it’s too thin, add more confectioners sugar. I love grating fresh lemon or orange zest into the glaze as well to add more fresh, bright flavor.

The rind of citrus fruits also contains vitamin C so you can feel good knowing you’re getting a little more of that too!

almond flour gingerbread muffins

Pumpkin Gingerbread Muffins with Lemon Glaze

Maggie Michalczyk, RDN
Extra flavorful and fluffy, you’ll love this festive gingerbread spin on a classic pumpkin muffin! Made gluten free with simple ingredients, these muffins are the perfect healthier treat to bake up in December. 
5 from 1 vote
Prep Time 10 minutes
Cook Time 22 minutes
Servings 12 muffins


For the muffins: 

  • 1 cup oat flour
  • 1 cup blanched almond flour
  • 2 tsp. pumpkin pie spice
  • 1 tsp. cinnamon
  • 1 tsp. ground ginger
  • 1/4 tsp. nutmeg
  • 1/4 tsp. salt
  • 3/4 tsp. baking soda
  • 2 eggs lightly beaten
  • 1/3 cup pumpkin puree
  • 1/3 cup maple syrup
  • 2 tbsp. molasses
  • 1 tsp. vanilla extract
  • 1/2 cup unsweetened almond milk
  • 1 tsp. coconut oil
  • 1 tsp.fresh lemon juice

for the lemon glaze:

  • 1/2 cup confectioners sugar
  • 1 1/2 tsp. maple syrup
  • 2 tsp. lemon juice
  • fresh lemon or orange zest


  • Preheat oven to 350 degrees F. Line 12 muffin cups with liners and spray the inside of the liners with nonstick cooking spray so the muffins do not stick.
  • In a medium bowl, whisk together oat flour, almond flour, pumpkin pie spice, cinnamon, ginger, nutmeg, salt and baking soda.
  • In a separate large bowl, mix together eggs, pumpkin puree, maple syrup, molasses, vanilla extract, almond milk, coconut oil and lemon juice until smooth and well combined. Pour the wet ingredients into the dry ingredients and use a wooden spoon stir until just combined.
  • Divide batter evenly in each muffin tin. Bake for 20-22 minutes.
  • While the muffins are baking whisk together the ingredients for the lemon maple glaze. It should be thick enough to drizzle. If too thick, add a little more lemon juice or almond milk to thin it out. 
  • Remove muffins from the oven and let cool. Use a fork to drizzle icing on top of each. Top with extra pumpkin pie spice and fresh lemon or orange zest. Enjoy! 
Keyword pumpkin muffins; pumpkin gingerbread muffins; gingerbread muffins; gluten free pumpkin muffins

This recipe was originally posted in November of 2020 and updated in December 2021.

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gingerbread muffins with lemon glaze
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Recipe Rating

6 thoughts on “Pumpkin Gingerbread Muffins with Lemon Glaze

  1. Delicious! These satisfy my sweet tooth without a lot of sugar, and combine some of my favorite fall flavors. I had to bake about 28 minutes to get done, but maybe it was the silicone muffin cups I use.
    I LOVE ginger, so next time, I will grate some fresh ginger into the mix. Thank you for sharing this recipe.

  2. These are absolutely delicious 😋😋
    I am diabetic,so just drizzled some maple
    syrup and pumpkin pie spice on top😍
    Thanks for sharing the recipe 😁

  3. 5 stars
    Delicious!! I subbed the powdered sugar for sugar free! This is such a wonderful, healthier version of the typical-full of sugar-muffins! Thank you for sharing!