Baking/ Bread/ Breakfast/ Recipe

Whole Wheat Lemon Poppy Seed Muffins

February 4, 2017 (Last Updated: July 2, 2019)

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Whole Wheat Lemon Poppy Seed Muffins!

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.

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 ingredients do I need for Whole Wheat Poppy Seed Muffins?

  • Butter
  • Sugar
  • Fresh lemon
  • Egg
  • Milk
  • Vanilla
  • Poppy Seeds
  • White Whole Wheat Flour
  • Baking Powder 
  • Salt

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 blueberry muffins, blackberry 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, Iā€™d love to hear about it! Leave a comment below and snap a picture and tag me on Instagram @beyondthechickencoop

5 from 2 votes
Whole Wheat Lemon Poppy Seed Muffin
Whole Wheat Lemon Poppy SeedMuffins
Prep Time
15 mins
Cook Time
18 mins
Total Time
33 mins

Whole Wheat muffins bursting with poppy seeds and fresh lemon flavor.

Course: Bread, Breakfast
Cuisine: American
Keyword: lemon poppyseed muffins, muffins with poppyseeds, whole wheat muffins
Servings: 10 Muffins
Calories: 226 kcal
Author: Kathy
  • 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
  1. In a large mixing bowl, combine butter and sugar.

  2. Mix in lemon zest, lemon juice, egg, milk and vanilla

  3. Mix in poppy seeds, whole wheat flour, baking powder and salt. Mix just until combined. 

  4. Measure into paper lined or greased muffin tins.

  5. Bake at 400 degrees for 15-18 minutes.

  6. Let cool slightly for 5 minutes and then remove from tin. Continue cooling on a baking rack. 

  1. Mix powdered sugar and lemon juice together. 

  2. While muffins are still warm, but not hot drizzle with glaze. 

Recipe Notes

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

Nutrition Facts
Whole Wheat Lemon Poppy SeedMuffins
Amount Per Serving
Calories 226 Calories from Fat 54
% Daily Value*
Fat 6g9%
Saturated Fat 3g19%
Cholesterol 13mg4%
Sodium 106mg5%
Potassium 237mg7%
Carbohydrates 41g14%
Fiber 2g8%
Sugar 22g24%
Protein 3g6%
Vitamin A 160IU3%
Vitamin C 0.6mg1%
Calcium 101mg10%
Iron 1.1mg6%
* Percent Daily Values are based on a 2000 calorie diet.



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  • 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
    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 šŸ™‚

    • 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!

  • Reply
    February 6, 2017 at 5:52 pm

    What a delicious and healthy recipe. Kathy! Love that these are made with whole wheat! Worth the effort, right?

    • Reply
      February 9, 2017 at 5:57 am

      They are delicious and the whole wheat flour keeps them healthy!

  • Reply
    karrie @ Tasty Ever After
    February 6, 2017 at 11:30 am

    Too funny! My Hubby loves lemon poppy seed muffins so I’ll have to make him this healthy version for breakfast this weekend!

  • Reply
    Anu - My Ginger Garlic Kitchen
    February 6, 2017 at 11:03 am

    These muffins look so nicely baked and delicious. Perfect way to start any morning. Love the fact they are made with whole-wheat. I wish I could grab a few of them right away. šŸ™‚

  • Reply
    February 6, 2017 at 10:45 am

    perfect breakfast right there! yum!

    • Reply
      February 7, 2017 at 5:21 am

      Muffins for breakfast are one of my favorites!

  • Reply
    Cheyanne @ No Spoon Necessary
    February 6, 2017 at 9:27 am

    Great minds! I made lemon poppy seed muffins over the weekend! Obviously I MUST try yours because they look wonderful, Kathy! Besides, one can NEVER have too many muffins in their arsenal! Cheers!

    • Reply
      February 7, 2017 at 5:21 am

      We just must think alike! šŸ™‚

  • Reply
    Dawn - Girl Heart Food
    February 6, 2017 at 5:09 am

    Hahaha! Not me…that’s funny, but totally know what you mean. Funny thing about that Not me person, isn’t it šŸ˜‰ ? Lemon poppy seed muffins/loaf is one of my favourite things and love that you made a whole wheat version. Wish I had one right now (ok, maybe two) !

    • Reply
      February 6, 2017 at 7:24 am

      Sometimes things just turn out! I was so relieved that everyone loved these muffins! This recipe is a definite keeper!

  • Reply
    David @ Spiced
    February 6, 2017 at 4:57 am

    Hahaha! I love that you have a new addition to the house. Hopefully “not me” doesn’t eat too many of these muffins because they sound delicious! I love baking with whole wheat flour, and I can totally see how the lemon poppyseed + whole wheat combo would work well. Yum!

    • Reply
      February 6, 2017 at 7:19 am

      I beginning to wonder because they disappeared awfully darned quick!

  • Reply
    Geraldine | Green Valley Kitchen
    February 5, 2017 at 8:07 pm

    Lol, Kathy, if my dog could talk she would say “not me” whenever I find one of her toys completely destroyed with fluff all over the house. Glad you had a successful result with the wheat flour – I’ve had my share of “not me” mistakes too!

    • Reply
      February 6, 2017 at 7:11 am

      That “Not Me” seems to be everywhere! šŸ™‚

  • Reply
    Nicoletta @sugarlovespices
    February 5, 2017 at 8:02 am

    That was funny, Kathy! Sometimes, even here, between Loreto and I we have this “it wasn’t me!” thing going on ?. Your muffins look as delicious as if they were made with all purpose flour, and maybe with a more interesting texture paired with the lemon and poppy seeds. Love it!

    • Reply
      February 6, 2017 at 7:10 am

      Thanks, Nicoletta! The whole wheat flour does add a bit of flavor and texture plus it just make them a bit healthier.

  • Reply
    Mary Ann | The Beach House Kitchen
    February 4, 2017 at 2:39 pm

    Well, at least “not me” did a good thing for once right?! Now you know you can use both flours and they are equally as delicious Kathy! These sound wonderful and lemon poppy is always such a good combo!

    • Reply
      February 4, 2017 at 3:07 pm

      Now if I could just get him/her to do the dishes! šŸ™‚

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