With the addition of an entire lemon, these whole lemon muffins are boldly-flavored without being tart. And with big, domed tops? We’re talking dreamy bakery muffins here!

Whole Lemon Muffins

When I set out to make muffins, I want a muffin.

Not some wimpy, under-flavored piece of cake trying to be a muffin. 

The Ideal Muffin

My ideal muffin has got to be to boldly flavored. It’s got to have a soft crumb. And for Pete’s sake, it’s got to have a big, bakery style muffin top!

Overhead photo of 3 Whole Lemon Muffins on a white plate.

Essentially, The Pastry Queen has got my ideal muffin covered and it was just my luck to be able to choose these muffins this week for our group’s baking recipe.

A Whole Lemon?

With the addition of an entire lemon (yes, skin, pith, juice, and pulp), these aptly named Whole Lemon Muffins have got my “bold” requirement covered while miraculously not being overly tart, as I feared they might be.

Pinterest Image of Whole Lemon Muffins

With little pieces of lemon floating around the muffin, they are the perfectly-flavored lemon muffin. 

The addition of yogurt yields a soft crumb. Oh so soft and tender!

And because you’ll fill the batter up to the top of the muffin cup, you’ll be left with a great big muffin top even though they’re baked in a standard-size muffin tin. It’s the BEST part of the muffin!

I added a few teaspoons of poppy seeds to these whole lemon muffins because what’s a lemon muffin without the poppy seeds? With the poppy seeds and giant muffin tops, these are the bakery style muffins of my dreams.

More Bakery Style Muffins You’ll Absolutely Love to Eat

Three Whole Lemon Muffins in yellow muffin papers are on a white plate.

Whole Lemon Muffins

Yield: 18 muffins
Prep Time: 15 minutes
Bake Time: 20 minutes
Total Time: 35 minutes

Whole Lemon Muffins make use of an entire lemon (minus the seeds) in one big batch of bakery style muffins. They're soft with big domes, studded with poppy seeds, and covered in a lemon glaze. Can a lemon poppy seed muffin recipe get any better than that?


For the muffins:

  • 1 medium lemon
  • 1 cup walnuts or pecans (optional)
  • 1 cup (2 sticks) unsalted butter, at room temperature
  • 1 ½ cups granulated sugar
  • 3 large eggs
  • 2 tsp vanilla extract
  • 2 ¾ cups all-purpose flour
  • 1 tsp baking soda
  • 1 tbsp baking powder
  • 1 tsp salt
  • 1 ⅔ cups (16 oz) plain whole-milk yogurt
  • 2 tbsp poppy seeds

For the glaze:

  • 1 cup powdered sugar
  • Freshly squeezed juice of 2 small lemons
  • ½ tsp vanilla extract


  1. To make the muffins: Preheat the oven to 350° F. Grease two standard-size muffin tins with butter or cooking spray, or line them with muffin wrappers; set aside.
  2. Wash and dry the lemon, cut it into quarters, and remove the seeds. Process the quartered lemon (skin, pith, and all) in a food processor fitted with a metal blade for 1 minute or more, until it is completely ground up. Scrape the lemon into a medium bowl. Without washing the food processor, add the walnuts and pulse 10 to 12 times, if using. (The nuts will clean the processor bowl.) Add the walnuts to the processed lemon and stir to combine. Set the lemon purée or the lemon-nut mixture aside to be used later.
  3. Using a stand mixer fitted with a paddle attachment, cream the butter on medium-high speed, about 1 minute. Scrape down the sides of the bowl. Add the sugar and mix on medium-high until light and fluffy, about 2 minutes. Scrape down the bowl. Add the eggs all at once and beat on medium speed about 1 minute. Blend in the vanilla on medium for about 30 seconds, until well incorporated.
  4. In a medium bowl, stir together the flour, baking soda, baking powder, and salt. Add one-third of the flour mixture to the batter and beat on medium-low speed just until it is incorporated. Add half of the yogurt and beat on medium speed until it is just incorporated. Repeat with the remaining dry ingredients and yogurt. Gently stir the lemon purée or lemon-nut mixture into the batter. Spoon the batter into the muffin pans, filling each cup just to the top.
  5. Bake for 18 to 22 minutes, until they are slightly browned and a toothpick inserted in to the middle of a muffin comes out clean. Transfer the muffin tins to wire racks and allow the muffins cool in their pans for about 5 minutes. Remove the muffins from the pans and transfer them to the racks. Place a long piece of foil or parchment paper underneath the racks.
  6. To make the glaze: Combine the sugar, lemon juice, and vanilla in a medium bowl. Drizzle the glaze over the warm muffins. The glaze will harden in about 15 minutes. These are at their very best served warm

STORAGE: If wrapped tightly in plastic wrap once completely cool they will still taste great for about 3 days. They can also be frozen up to 3 weeks.


adapted from The Pastry Queen by Rebecca Rather

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Leave a Comment

  • June 27, 2011 at 8:54 AM

    I feel like I can almost taste these…look at that glaze! I cannot wait to try them.

  • June 27, 2011 at 6:34 PM

    Wow these muffins look amazing!!! Love the lemon and poppy seeds. Yum!

  • Chiara
    June 28, 2011 at 11:47 PM

    Looks delicious! I’d like to try half a recipe too but I’m curious as to how you handled the 3 eggs – did you just use 1 egg?

    • smellslikehome
      June 28, 2011 at 11:53 PM

      Chiara: I used one whole egg and lightly whisked another egg (in a separate bowl) then just used half of that egg.

  • June 29, 2011 at 10:21 AM

    These look wonderful! We love muffins here, and I have never tried a lemon muffin before. Saving this for later!

  • June 29, 2011 at 10:48 AM

    I never made good muffins. Your muffins look amazing though. So, I’m going to try again 😛

  • June 29, 2011 at 11:15 AM

    I love the idea of adding the entire lemon, I can just imagine the flavor! The last time I made lemon muffins they were too boring, this would be perfect!

  • June 29, 2011 at 11:30 AM

    Wow these look delectable! I love the Pastry Queen!

  • June 29, 2011 at 12:17 PM

    Wow!! I think this is like summer in a muffin! A WHOLE lemon makes me think summa, summa, summa time!

  • June 29, 2011 at 1:16 PM

    I love muffins with a strong taste too so I must try these ones with whole lemons! They look amazing

  • June 29, 2011 at 2:52 PM

    These sound so good! I love lemon muffins and will be printing this out right NOW!

  • June 29, 2011 at 5:21 PM

    I am a sucker for anything with lemon in, and all too often i wished there was just that bit more of an OOMPF to lemony goods. The fact this has a whole lemon in….just send some to me now please?! Everything about this post is delicious 🙂 This is definitely a recipe that is being saved and baked hopefully sooner rather than later!

  • June 29, 2011 at 6:09 PM

    I love me some lemony muffins! And I like your idea of using sugar vs the glaze. I got caught up with the 24×24 last weekend so I’m going to make them this weekend.

  • June 29, 2011 at 8:18 PM

    Those look so delicious! I love that they have a whole lemon in them. And that glaze looks amazing!

  • June 29, 2011 at 9:40 PM

    These muffins are definitely not shy!

  • June 30, 2011 at 1:40 PM

    I also like my muffins the way that you described them… and a BIG muffin top! 🙂
    I especially love a citrus muffin…these sound yummy-good!

  • July 1, 2011 at 12:19 PM

    Oooh, tart lemon muffins – I’m in love! Can’t wait to try this, thanks for sharing!

  • July 1, 2011 at 11:59 PM

    I so want those muffins. Lemon anything always makes me happy. I have a sweet treat linky party going on at my blog and I’d love it if you’d come by and link up your muffins. http://sweet-as-sugar-cookies.blogspot.com/2011/07/sweets-for-saturday-23.html

  • August 1, 2011 at 9:18 PM

    These look amazing. Although instead of the glaze, what about a spoonful of lemon curd? (I have a lot of lemons on my hands!)

    • smellslikehome
      August 2, 2011 at 5:39 AM

      Deidre: I’m sure lemon curd would be wonderful.

  • February 21, 2013 at 9:24 AM

    how do these freeze? My husand is convinced he doesn’t like lemon muffins, but we’ll see. lol heatha100@gmail.com

    • February 21, 2013 at 3:04 PM

      I haven’t frozen them but I’m sure they will freeze ok.