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Home » Muffins

Published: Feb 4, 2017 · Modified: Feb 3, 2025 by Kathy

Whole Wheat Lemon Poppy Seed Muffins

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Muffins with poppy seeds and a glaze.

Whole Wheat Lemon Poppy Seed Muffins! These tasty muffins are packed with lemon flavor and poppy seeds and drizzled with a lemon glaze.

Perfect for breakfast, brunch or tea.

A poppy seed muffin topped with a drizzled glaze.

Whole wheat muffins

I don't often make muffins with whole wheat flour. But these lemon poppy seed muffins are made with 100% whole wheat flour. They aren't heavy or dense like you'd expect because I used white whole wheat flour.

Does that sound like an oxymoron? Yep, but it's not! White whole wheat flour is milled from a different grain than regular whole wheat flour.

White whole wheat flour is from white wheat berries. They are lighter and slightly sweeter than the traditional red wheat berry. It has all the benefits of whole wheat flour.

These whole wheat lemon poppy seed muffins are a great way to start the day. I've added a lemon glaze, which is optional. But you won't want to skip it. The glaze adds so much lemony flavor.

Plus these muffins don't contain a lot of sugar. So a little extra on the top isn't going to put you over the edge! You can add as much glaze as you'd like. If you'd like less sugar, just drizzle a small amount over the top of each muffin.

If you love poppy seed muffins, you'll also want to try these Almond Poppy Seed Muffins!

A poppy seed muffin cut in half.

My favorite part about these muffins, besides the amazing taste, is no one will ever know they are made with whole wheat flour.

Key ingredients

This section reviews the best ingredients and substitutions for this recipe. For an exact list of ingredients and quantities, check the recipe card below.

  • White Whole Wheat Flour - you could also use all-purpose flour
  • Poppy Seeds
  • Lemon - you'll want a fresh lemon for the zest and the juice
  • Butter and Oil - I've added a bit of oil to help keep these muffins moist
  • Sugar - granulated sugar for the muffins and powdered sugar for the glaze

Making lemon poppy seed muffins

  • Combine butter, oil and sugar together in a mixing bowl. Mix until light and creamy
  • Add lemon zest, lemon juice, egg, vanilla and milk. Mix well.
Butter and sugar in a mixing bowl.
Eggs and milk added to a mixing bowl.
  • Add flour, baking powder, baking soda, salt and poppy seeds. Mix just until the ingredients come together. Turn off mixer and continue mixing ingredients together with a spatula.
Flour with poppy seeds in a mixing bowl.
Mixed muffin dough in a bowl.
  • Place in muffin tins lined with paper liners or sprayed with a nonstick spray
  • Bake in a preheated 400°F oven for 12-14 minutes. Use a toothpick to test muffins.
  • Remove from oven and cool for 1-2 minutes in muffin tins then remove muffins and continue cooling on a baking rack.
  • Make glaze by combining powdered sugar and lemon juice with a small whisk. Add enough lemon juice to make glaze pourable.
  • Drizzle glaze over warm muffins
Muffin batter in a muffin tin.
Muffins on a baking rack.

Recipe tips

  • Use softened, but not melted butter
  • The mixture may look slightly curdled when adding the lemon juice and milk. This is okay!
  • To save time (and a bowl) I will often add the flour, baking powder, baking soda and salt right to the wet ingredients. I then reach in with a small spoon (with the mixer OFF) and just give the dry ingredients a quick stir. This mixes up the salt and baking powder/soda so it's distributed throughout the flour.
  • Once the flour is added, just mix with the mixer a few times. You want the flour to just be barely mixed into the wet ingredients.
  • Turn the mixer off and then fold everything together with a spatula. You don't want to overmix or the muffins will become tough.
  • Oven temperatures vary, so baking times may vary.
  • Check muffins at 12 minutes and test with a toothpick. If needed, bake for 1-2 additional minutes.
  • Paper liners may be used for making the muffins or you can simply spray the muffin tin with nonstick spray

Frequently asked questions

Can I use all-purpose flour instead of white whole wheat flour in these muffins?

Yes, you can use all-purpose flour when making these muffins. Substitute the same amount of flour. Baking time may increase by 1-2 minutes.

How long will poppy seed muffins last?

The muffins will last 3-4 days. Once fully cooled place in an airtight container and store at room temperature.

More muffin recipes

Having a variety of muffins for breakfast makes breakfast extra special.

  • peach muffins
  • apple carrot muffins
  • blueberry muffins
  • banana blueberry muffins
  • bran muffins
  • blackberry muffins
  • peanut butter muffins
  • pear muffins
  • blackberry muffins
Muffins on a baking rack.

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!

  • Chocolate Banana Muffin with chocolate chips on a white plate.
    Chocolate Banana Muffins
  • Almond Poppy Seed Muffins on a baking rack.
    Almond Poppy Seed Muffins
  • Cranberry Banana Muffins on a small plate next to a cup of coffee.
    Cranberry Banana Muffins
  • An apple banana muffin on a small blue plate.
    Banana Apple Muffins
A poppy seed muffin topped with a drizzled glaze.

Whole Wheat Lemon Poppy Seed Muffins

Kathy Berget
Whole Wheat muffins bursting with poppy seeds and fresh lemon flavor.
4.85 from 13 votes
Print Recipe Pin Recipe Save Saved!
Prep Time 15 minutes mins
Cook Time 18 minutes mins
Total Time 33 minutes mins
Course Bread, Breakfast
Cuisine American
Servings 12 Muffins
Calories 199 kcal

Equipment

  • Measuring Cups
  • Measuring Spoons
  • Muffin Tin
  • Cooling Rack
Prevent your screen from going dark

Ingredients
 
 

  • ¼ cup butter (softened)
  • ½ cup sugar
  • 1 tablespoon oil (vegetable or canola)
  • 1 tablespoon lemon zest
  • 2 tablespoons lemon juice
  • 1 egg
  • 1 cup milk
  • ½ teaspoon vanilla
  • 2 Tablespoons poppy seeds
  • 2 cups white whole wheat flour
  • 2 teaspoons baking powder
  • ½ teaspoon baking soda
  • ¼ teaspoon salt

Glaze (optional)

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

Instructions
 

Muffins

  • Preheat oven to 400°F
  • In a large mixing bowl, combine butter, oil and sugar.
    ¼ cup butter, ½ cup sugar, 1 tablespoon oil
  • Mix in lemon zest, lemon juice, egg, milk and vanilla
    1 tablespoon lemon zest, 2 tablespoons lemon juice, 1 egg, 1 cup milk, ½ teaspoon vanilla
  • Mix in poppy seeds, whole wheat flour, baking powder and salt. Mix just until combined. 
    2 Tablespoons poppy seeds, 2 cups white whole wheat flour, 2 teaspoons baking powder, ½ teaspoon baking soda, ¼ teaspoon salt
  • Measure into paper lined or greased muffin tins.
  • Bake at 400 degrees for 12-14 minutes.
  • Let cool slightly for 1-2 minutes and then remove from tin. Continue cooling on a baking rack. 

Glaze

  • Mix powdered sugar and lemon juice together. 
    1 cup powdered sugar, 1-2 1ablespoons lemon juice
  • While muffins are still warm, but not hot drizzle with glaze. 

Notes

  • Use softened, but not melted butter
  • The mixture may look slightly curdled when adding the lemon juice and milk. This is okay!
  • To save time (and a bowl) I will often add the flour, baking powder, baking soda and salt right to the wet ingredients. I then reach in with a small spoon (with the mixer OFF) and just give the dry ingredients a quick stir. This mixes up the salt and baking powder/soda so it's distributed throughout the flour.
  • Once the flour is added, just mix with the mixer a few times. You want the flour to just be barely mixed into the wet ingredients.
  • Turn the mixer off and then fold everything together with a spatula. You don't want to overmix or the muffins will become tough.
  • Oven temperatures vary, so baking times may vary.
  • Check muffins at 12 minutes and test with a toothpick. If needed, bake for 1-2 additional minutes.
  • Paper liners may be used for making the muffins or you can simply spray the muffin tin with nonstick spray
 
This recipe has been updated 4/13/22

Nutritional Disclaimer:

Nutritional information is provided as a courtesy and should only be construed as an estimate rather than a guarantee. To obtain the most precise nutritional information in a provided recipe, you should calculate the nutritional information with the exact ingredients you are using when preparing the recipe using your preferred nutrition calculator.

Nutrition

Serving: 1muffinCalories: 199kcalCarbohydrates: 34gProtein: 4gFat: 6gSaturated Fat: 3gPolyunsaturated Fat: 1gMonounsaturated Fat: 1gTrans Fat: 1gCholesterol: 26mgSodium: 139mgPotassium: 142mgFiber: 2gSugar: 19gVitamin A: 171IUVitamin C: 2mgCalcium: 93mgIron: 1mg
Tried this Recipe? Tag me Today!Mention @BeyondTheChickenCoop or tag #beyondthechickencoop!

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Reader Interactions

Comments

  1. Kris D. says

    February 25, 2023 at 8:20 am

    Can whole wheat pastry flour(soft white wheat) be used also?

    Reply
    • Kathy says

      February 25, 2023 at 8:47 am

      Yes!

      Reply
  2. Norah says

    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
    • Kathy says

      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!
      Kathy

      Reply
  3. Fred G says

    April 29, 2019 at 8:25 am

    5 stars
    Great idea for anytime

    Reply
    • Kathy says

      April 29, 2019 at 5:35 pm

      I love muffins just about anytime!

      Reply
  4. Emily says

    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
    • Kathy says

      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!
      Kathy

      Reply
  5. Laura ~ Raise Your Garden says

    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
  6. allie says

    February 09, 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
    • Kathy says

      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
  7. Patti says

    February 08, 2017 at 11:28 pm

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

    Reply
    • Kathy says

      February 09, 2017 at 6:42 am

      They are a favorite for us too!

      Reply
  8. Ami@NaiveCookCooks says

    February 07, 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
    • Kathy says

      February 07, 2017 at 6:34 pm

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

      Reply
  9. Adina says

    February 07, 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
  10. Rachelle @ Beer Girl Cooks says

    February 06, 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
    • Kathy says

      February 09, 2017 at 5:58 am

      I guarded them closely!

      Reply
  11. Rahul @samosastreet.com says

    February 06, 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
    • Kathy says

      February 09, 2017 at 5:57 am

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

      Reply
  12. karrie @ Tasty Ever After says

    February 06, 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
  13. Anu - My Ginger Garlic Kitchen says

    February 06, 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. 🙂

    Reply
  14. Manali@CookWithManali says

    February 06, 2017 at 10:45 am

    perfect breakfast right there! yum!

    Reply
    • Kathy says

      February 07, 2017 at 5:21 am

      Muffins for breakfast are one of my favorites!

      Reply
  15. Cheyanne @ No Spoon Necessary says

    February 06, 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
    • Kathy says

      February 07, 2017 at 5:21 am

      We just must think alike! 🙂

      Reply
  16. Dawn - Girl Heart Food says

    February 06, 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 😉 ? 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
    • Kathy says

      February 06, 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
  17. David @ Spiced says

    February 06, 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
    • Kathy says

      February 06, 2017 at 7:19 am

      I beginning to wonder because they disappeared awfully darned quick!

      Reply
  18. Geraldine | Green Valley Kitchen says

    February 05, 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
    • Kathy says

      February 06, 2017 at 7:11 am

      That "Not Me" seems to be everywhere! 🙂

      Reply
  19. Nicoletta @sugarlovespices says

    February 05, 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
    • Kathy says

      February 06, 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
  20. Mary Ann | The Beach House Kitchen says

    February 04, 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
    • Kathy says

      February 04, 2017 at 3:07 pm

      Now if I could just get him/her to do the dishes! 🙂

      Reply
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I'm Kathy, and I love to create delicious recipes from scratch utilizing many ingredients that we grow and raise. I'm a recipe creator, food photographer, and cookbook author!

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