Liv’s Pumpkin Flax Muffins

These healthy whole wheat pumpkin flax muffins have the most tender crumb. They’re super moist and packed with delicious spice flavours, that are based off of my pumpkin cake with cream cheese frosting. These pumpkin muffins are delicious plain or you can add a smear of butter for a “complete” breakfast ;).

As these pumpkin muffins are packed with good fats and whole grains, they make a great snack for your older kids, toddlers or even babies! Both of my kids enjoy these although my son would prefer if they had chocolate in them. Muffins are the main thing I take for breakfast to eat between patients at work and these particular pumpkin muffins are great as they are quite filling.

I like trying to get some vegetables into my healthy bakes when I can and pumpkin is one of the easiest veggies to add (or are they a fruit? I never know). Pumpkin helps create the softest, most tender crumb and these pumpkin muffins are no exception. Even with the addition of ground flaxseed, these muffins are still so moist, you’ll forget they’re a healthier option. If you’re interested in other muffins with veggies thrown in, check out my healthier double chocolate zucchini muffins or my cream cheese filled carrot muffins.

How to Store Muffins

When storing muffins, the first step is to ensure they are fully cooled. Storing warm muffins leads to excess moisture which will ruin the texture of your muffins and cause them to get gummy and soggy, especially on the tops. 

As muffins are generally and hopefully very moist, the easiest way to keep them from getting soggy is to store them with paper towels. 

Place a paper towel on the bottom of an airtight container or bag. I like to use an extra large reuseable bag. Then place the muffins on top in a single layer and lay an additional paper towel on top of them. Store them at room temperature for up to 3 days.

How to Freeze Muffins

The best thing about all my healthy muffins and quick breads is they freeze well. They’re an easy thing to whip up and meal prep for the week or month! When freezing muffins, you’ll again want to ensure they’re completely cooled. 

Once cooled, place a paper towel on the bottom of an airtight container or bag. I like to use a freezer safe extra large reusable bag. Place the muffins on top in a single layer and then place another paper towel on top. The paper towel helps to keep the excess moisture away from the muffins and helps ensure they don’t get freezer burnt. Store like this for up to 3 months.

When you’re ready to eat one or all of them, let thaw at room temperature for a couple hours or heat in the microwave in 20 second increments. Be cautious if using the microwave when feeding children or toddlers, it can leave hot spots.

How to Properly Measure Flour

So when it comes to measuring flour, the most accurate and easiest way is to use a kitchen scale. I always use a scale and could never go back to measuring in cups. It’s such a hassle and way more dishes!

If you don’t own a scale, there are a couple steps to properly measure flour as it becomes compacted just sitting in the bag or container. I highly recommend you follow these as just scooping flour out of the bag can potentially lead to at least an additional 1/4 cup of flour. This equals dry and dense baked goods which is not what anybody is going for.

1. Fluff the flour by giving it a mix with a whisk or fork.

2. Spoon the flour into your measuring cup.

3. Level the excess flour off using a butter knife. (With the back of the knife level to the top of the measuring cup, run it over top, pushing the excess flour back into it’s container.)

4. Repeat until you’ve measured the amount the recipe calls for.

Baking Tips

  • Don’t overmix the batter! Fold the wet and dry ingredients together until just combined. This ensures a tender crumb rather than a tight, dense muffin.
  • The measurements for these pumpkin muffins are based off of canned pumpkin puree. I have never tested them with fresh pumpkin but would guess it would have different weights so am unsure of how they’d turn out.
  • I create my recipes based off weights so I recommend measuring by weights if you own a scale. It’s actually so much easier and makes for much less cleanup. I wish I had baked by weight from the beginning, I could never go back now.

Equipment Needed

  • Cupcake pan
  • Muffin liners or spray
  • Whisk
  • Spatula (or other utensil to fold batter)
  • Large mixing bowl
  • Medium mixing bowl

Other Muffin Recipes

Pumpkin Oatmeal Chocolate Chip Muffins

Pear Sauce Chocolate Chip Muffins

Chocolate Almond Banana Muffins

My song for you guys today is one I love dancing to while baking. Hope you get the chance to dance around your kitchen while you whip up these amazing pumpkin muffins! Here’s I Don’t Feel Like Dancin’ by Scissor Sisters. Happy Baking!! **Disclaimer: Liv’s Little Muffins owns no rights to this song.

Don’t forget to leave a STAR REVIEW if you try my recipe! Follow me on Facebook or tag me on instagram @livslittlemuffins. Find more ideas on my Pinterest or Whisk.

Liv’s Pumpkin Flax Muffins

Olivia Daly
These healthy whole grain pumpkin flax muffins have the most tender crumb and are packed full of pumpkin spice flavours.
5 from 1 vote
Prep Time 10 minutes
Cook Time 22 minutes
Total Time 32 minutes
Course Breakfast, Snack
Servings 12


  • 2 cups (240g) whole wheat flour
  • 1/2 cup (40g) ground flaxseed
  • 2 1/2 tsp baking powder
  • 3/4 tsp baking soda
  • 3 tsp ground cinnamon
  • 1/2 tsp ground cloves
  • 1/4 tsp ground allspice
  • 1/4 tsp ground cardamom
  • 1/2 tsp ground nutmeg
  • 1/4 tsp salt
  • 2 large eggs
  • 2/3 cup (120g) brown sugar, packed
  • 1/2 cup (90g) canola oil
  • 1 3/4 cup (350g) pumpkin puree
  • 1/3 cup (75g) unsweetened oat milk (or any milk)
  • 1 tsp vanilla extract
  • Zest from 1 lemon


  • Preheat your oven to 350 degrees. Line or spray 12 muffin tins.
  • In a medium mixing bowl, combine the flour, ground flaxseed, baking powder, baking soda, ground cinnamon, ground cloves, ground allspice, ground cardamom, ground nutmeg and salt. Set aside.
  • In a large mixing bowl, whisk together the eggs and brown sugar for 30 seconds.
  • Add in the canola oil, pumpkin puree, milk and vanilla extract. Whisk until combined. Whisk in the lemon zest.
  • Pour the dry ingredients into the wet mixture and fold together until just combined. Don't overmix or you'll end up with tough, dense muffins.
  • Divide the batter among 12 muffin tins and bake for 20-23 minutes or until a toothpick comes out clean.
  • Let the muffins cool in the tins for 5 minutes then fully cool on a cooling rack. Store in an airtight container for up to 3 days or in the freezer for up to 3 months. Enjoy!!
Keyword healthy pumpkin flax muffins, healthy pumpkin muffins, pumpkin flax muffins, pumpkin muffins, whole wheat pumpkin muffins

Nutrition Facts

Serving Size1muffin
Amount Per Serving
% Daily Value *
Total Carbohydrate29g
Dietary Fiber5g
Total Fat10g
Saturated Fat1g
Trans Fat0.03g


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