Baking/ Bread/ Breakfast/ Recipe

Whole Wheat Lemon Poppy Seed Muffins

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

This post may contain affiliate links, see my Privacy Policy.

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

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.ย 


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.



You Might Also Like


  • 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. ๐Ÿ™‚

  • Reply
    [email protected]
    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! ๐Ÿ™‚

  • 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 ๐Ÿ˜‰ ? 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! ๐Ÿ™‚

  • 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! ๐Ÿ™‚

    1 2

    Leave a Reply

    Recipe Rating