Baking/ Bread/ Breakfast/ Muffins

Whole Wheat Lemon Poppy Seed Muffins

February 4, 2017 (Last Updated: November 5, 2020)

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Whole Wheat Lemon Poppy Seed Muffins! These tasty muffins are packed with lemon flavor and poppy seeds. To make them even tastier, they are drizzled with a light lemon glaze. 

Poppy seed muffin with a glaze drizzled over the top of the muffin.

These whole wheat lemon poppy seed muffins were a bit of a surprise. In my house we have a “Not Me” who seems to have become part of our family! A plateful of muffins topped with a drizzle of icing.

We have all sorts of random things that happen: a dirty cup gets left on the counter, an empty box of crackers is left in the pantry, a wet towel on the bathroom floor…. Yet every time I ask, “Who left the cup here?” I get the same answer from all my children! “NOT ME!”

I kid you not! No one ever seems to have ever made the mess! I believe Not Me has moved in with us!

A poppy seed muffin broken in half on a white plate.

I store my flour in a large plastic container with a sealing lid. It only ever has regular all-purpose flour in it. Somehow whole wheat white flour was poured into the container! I am blaming Not Me!

I was making lemon poppy seed muffins and didn’t notice that I used whole wheat until the batter was mixed. Whole wheat white flour looks very similar to regular all purpose flour so I wasn’t able to spy a difference. It was too late to undo the flour so I just baked them as is and hoped for the best.

Wouldn’t you know it? They turned out amazing and received full approval from my kids! They are always my taste testers. They never say Not Me when I ask, “Who is ready for a muffin?”

Fresh muffins resting on a baking rack with a drizzle of icing on top of muffins.

What is white whole wheat flour?

White wheat flour is milled from white wheat berries instead of the red wheat berries that makes traditional whole wheat flour. The white wheat berries are slightly sweeter and lighter in color and flavor.  White whole wheat flour has all the nutritional value as traditional whole wheat flour. 


Having a variety of muffins for breakfast makes breakfast extra special. How about making these peach muffins, blueberry muffins, bran muffins, blackberry muffins, peanut butter muffins and pear muffins?

Don’t forget to PIN for later! Muffins with a thin icing dripping over the top of the muffins.

If you make this recipe, I’d love to hear about it! Leave a comment below and snap a picture and tag me on Instagram @beyondthechickencoop

Be sure to check out all my delicious muffin recipes!

Muffins filled with poppy seeds and topped with a thin icing over the top of the muffins.

Whole Wheat Lemon Poppy SeedMuffins

Whole Wheat muffins bursting with poppy seeds and fresh lemon flavor.
4.34 from 3 votes
Prep Time 15 mins
Cook Time 18 mins
Total Time 33 mins
Course Bread, Breakfast
Cuisine American
Servings 10 Muffins
Calories 226 kcal


  • 1/4 cup butter (softened)
  • 1/2 cup sugar
  • zest from one lemon
  • juice from one lemon
  • 1 egg (lightly beaten)
  • 1/2 cup milk
  • 1/2 teaspoon vanilla
  • 2 Tablespoons poppy seeds
  • 2 cups white whole wheat flour
  • 1 Tablespoon baking powder
  • 1/4 teaspoon salt

Glaze (optional)

  • 1 cup powdered sugar
  • 1-2 Tablespoons lemon juice (fresh squeezed)



  • In a large mixing bowl, combine butter and sugar.
  • Mix in lemon zest, lemon juice, egg, milk and vanilla
  • Mix in poppy seeds, whole wheat flour, baking powder and salt. Mix just until combined. 
  • Measure into paper lined or greased muffin tins.
  • Bake at 400 degrees for 15-18 minutes.
  • Let cool slightly for 5 minutes and then remove from tin. Continue cooling on a baking rack. 


  • Mix powdered sugar and lemon juice together. 
  • While muffins are still warm, but not hot drizzle with glaze. 


White whole wheat flour is a whole grain flour milled from white wheat berries. 


Calories: 226kcalCarbohydrates: 41gProtein: 3gFat: 6gSaturated Fat: 3gCholesterol: 13mgSodium: 106mgPotassium: 237mgFiber: 2gSugar: 22gVitamin A: 160IUVitamin C: 0.6mgCalcium: 101mgIron: 1.1mg
Keyword lemon poppyseed muffins, muffins with poppyseeds, whole wheat muffins
Tried this recipe?Leave a comment and let me know what you think.



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  • Reply
    May 23, 2020 at 7:26 pm

    3 stars
    I have made these twice and both times the batter is waaaaaaay too dry so I’ve added more milk and turned out great. Also added some lavender which was very tasty.

    • Reply
      May 24, 2020 at 5:08 am

      Hi Norah,
      Thanks for your comment. I’m sorry these were so dry for you, but I’m glad you’ve figured out a solution. The lavender sounds like a tasty addition!

  • Reply
    Fred G
    April 29, 2019 at 8:25 am

    5 stars
    Great idea for anytime

    • Reply
      April 29, 2019 at 5:35 pm

      I love muffins just about anytime!

  • Reply
    January 10, 2018 at 8:30 am

    5 stars
    I just made these last night! Really delicious. I have a quick question, though. The ingredients call for baking soda, but then the directions say baking powder. Should I be including baking powder or baking soda in the recipe? Thanks!

    • Reply
      January 10, 2018 at 7:18 pm

      Hi Emily,
      I’m so glad you loved these muffins. It looks like I made an error when typing up this recipe. I used baking powder. The recipe will be updated to reflect the accurate ingredients. Thanks so much for catching my error!

  • Reply
    Laura ~ Raise Your Garden
    February 10, 2017 at 5:46 am

    Hi Kathy! I’m sort of a dessert snob, so I eat very little dessert, but lemon & poppyseed is my ultimate weakness. These look so very good!

  • Reply
    February 9, 2017 at 12:28 pm

    Too funny, we have a Not Me at our house too. (Wonder if they’re related???) Wonderful to discover that these WW muffins got the stamp of approval from the kids too. That’s a big win. I often sub in a white whole wheat flour for nearly all my recipes that call for all purpose flour, no one even seems to notice. Yay. Your glaze is so pretty on thee muffins Kathy! Wish I had one right now. We are halfway through a big snowstorm and already have a foot on the ground!

    • Reply
      February 10, 2017 at 5:05 am

      I like using white whole wheat flour too. It has such a light taste and all the extra nutrients that make me feel good!

  • Reply
    February 8, 2017 at 11:28 pm

    Lemon Poppy Seed Muffins are my oldest son’s favorite. I can’t wait to try this recipe.

    • Reply
      February 9, 2017 at 6:42 am

      They are a favorite for us too!

  • Reply
    [email protected]
    February 7, 2017 at 10:48 am

    These muffins look amazing Kathy! My husband loves poppy seed muffins but the store ones are so full of butter and all purpose flour!! Can’t wait to give these a try 🙂

    • Reply
      February 7, 2017 at 6:34 pm

      Thanks, Ami! I hope he loves them as much as we do!

  • Reply
    February 7, 2017 at 10:13 am

    A happy accident! I would love one of those muffins, I’ve just realized I haven’t made any muffins in a long time.

  • Reply
    Rachelle @ Beer Girl Cooks
    February 6, 2017 at 6:38 pm

    Ha! We always called the “not me” in our house “that dang troll.” I’m pretty sure the troll and all the not me creatures would come running to try these lemon poppy seed muffins!

    • Reply
      February 9, 2017 at 5:58 am

      I guarded them closely!

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