These gluten free poppy seed muffins make the perfect grab and go breakfast, snack, or dessert!

This post contains affiliate links; this means if you purchase an item linked, I may receive a small commission at no extra cost to you. Click here to learn more about my disclosure policy.

A muffin tin full of poppyseed muffins

If you’ve ever made a trip (or 100) to Costco, you know about the muffins.

They come in packs of 12 gigantic muffins that are basically 4 normal sized muffins in one. The flavors rarely change but never disappoint with combination packs with either pumpkin, maple, blueberry, or poppy seed muffins.

My parents only bought the muffins on special occasions; over the holidays, for parties at our house or when family came to visit. I would wake up at the crack of dawn, sneak downstairs and enjoy half with a big glass of milk.

Now, when I crave something sweet, I make these gluten free poppy seed muffins!

A bowl of poppyseeds

Poppy Seeds

When I first started recipe testing for these, I assumed the process would go as smoothly as any other muffin recipe.

Hunting down poppy seeds proved to be more challenging than expected and after what felt like 10 trips to different grocery stores, I threw in the towel and headed online.

I finally caved and bought these poppy seeds by Bob’s Red Mill (one of my favorite brands) on Amazon.

Side Note: If you know a store where I can find these, let me know in the comment section below!

A bowl of poppyseed muffin batter

Other Killer Muffin Recipes

Before you commit to just one muffin recipe, allow me to encourage you to live your best Costco loving life and try 1 more of my all time, favorite muffin recipes:

A basket of gluten free poppyseed muffins
A muffin tin full of poppyseed muffins and a hand holding one with a bite taken
clock clock iconcutlery cutlery iconflag flag iconfolder folder iconinstagram instagram iconpinterest pinterest iconfacebook facebook iconprint print iconsquares squares iconheart heart iconheart solid heart solid icon
A muffin tin full of poppyseed muffins

Gluten Free Poppy Seed Muffins

5 Stars 4 Stars 3 Stars 2 Stars 1 Star No reviews
  • Author: Salima Benkhalti
  • Prep Time: 15 minutes
  • Cook Time: 20 minutes
  • Total Time: 35 minutes
  • Yield: 12 muffins 1x
  • Category: dessert
  • Method: baked
  • Cuisine: american



For the Muffins:

  • 3 cups gluten free flour
  • 1/2 tsp baking soda
  • 1 tbsp baking powder
  • 3/4 cup sugar
  • a pinch of salt
  • 3 tbsp lemon zest
  • 1/4 cup poppy seeds
  • 2/3 vegetable oil
  • 1 tbsp maple syrup
  • 2 eggs
  • 1 1/2 cup greek yogurt (honey or plain)
  • 1 tbsp raw sugar 

For the Glaze:

  • 4 tbsp powdered sugar
  • 4 tbsp oat milk 


  1. Preheat your oven to 375 degrees and grease your muffin tin
  2. In a large bowl, combine your dry ingredients (flour, baking soda, baking powder, salt, lemon zest, poppy seeds) with your sugar. Mix well. 
  3. In a smaller bowl, combine wet ingredients (oil, eggs, yogurt) and mix well. Fold the wet ingredients into the larger bowl with the dry ingredients. Fill the muffin tins 3/4 way. Sprinkle with raw sugar and bake for 15-20 minutes or until a toothpick comes out clean. 
  4. Make the glaze. Whisk oat milk and powdered sugar together. Once muffins have cooled for at least 20 minutes, pour the glaze over muffins and sprinkle with poppy seeds and lemon zest. Enjoy!