Whole Grain Vanilla Cupcakes with Lemon Honey Frosting


Recipe Intro From lisathompson

These whole grain vanilla cupcakes with lemon honey frosting marry wholesome ingredients and bright flavors together in an unexpected way. Perfect for those looking to indulge in a healthier treat, these cupcakes are made with whole wheat flour and almond meal, complemented by the zesty freshness of lemon and orange. Topped with a lemon honey frosting, these cupcakes are perfect for a Spring celebration.

Recipe Description

These vanilla cupcakes feature wholesome ingredients that elevate this classic bakery treat. The combination of whole wheat flour and almond meal creates a hearty base, while the buttermilk, vanilla, lemon zest, and orange zest add layers of citrusy flavor. The creamy lemon honey frosting provides a sweet and tangy finish.

Pair these sunny cupcakes with iced tea or lemonade. Use this vanilla cupcake recipe as your go-to base for different toppings, such as fudge frosting, lemon curd, or a simple vanilla buttercream.

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  • Whole Grain Vanilla Cupcakes with Lemon Honey Frosting Ingredients
  • Test Kitchen Notes
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  • Recipe Card

Whole Grain Vanilla Cupcakes with Lemon Honey Frosting Ingredients

Everything you need to make whole grain vanilla cupcakes.

  • Whole Wheat Flour (or white whole wheat): Both options add a nutty flavor and a slightly denser texture compared to all-purpose flour. You can substitute all-purpose flour for whole wheat flour or white whole wheat flour in equal amounts for a lighter texture.

    Almond Meal: Adds a nutty richness, subtle crunch, and flavor to this cupcake recipe. If you're allergic to nuts or prefer a different flavor, you can substitute almond meal with an equal amount of finely ground oats or hazelnut meal.

    Vanilla Bean Paste: Unlike traditional vanilla extract, this paste features real vanilla bean seeds, imparting a visually appealing speckled texture and an intensified vanilla essence. If you don't have vanilla bean paste, you can use an equal amount of vanilla extract.

Test Kitchen Notes

  • Homemade Vanilla Extract: Apart from using vanilla bean paste use a homemade vanilla extract. Simply submerge vanilla beans in vodka or bourbon and let them sit for several weeks, shaking the bottle occasionally. Strain before using, and use the same amount as store-bought vanilla extract in the recipe.

    Decorative Touch: Berries and kumquats add a burst of color and contrast in texture. adding edible flowers such as lavender, rose, or chamomile add visual appeal and infuse a subtle floral essence.

    Top it! For a professional-looking finish, use a cookie scoop to apply the frosting to the top of each cupcake. This ensures even portions and a neat presentation.


What is the secret to moist cupcakes?

How to make the perfect cupcake?

Is it better to make cupcakes with oil or butter?

What is the difference between yellow cake and vanilla cake?

Prep time 35mins
Cook time 22mins
Serves or Makes: 12 cupcakes

Recipe Card


  • 1 1/4 cups whole wheat flour or white whole wheat flour
  • 1/2 cup almond meal
  • 1 teaspoon baking powder
  • 1/2 teaspoon baking soda
  • 1/2 teaspoon kosher salt
  • 1 cup buttermilk (or non-dairy milk stirred with 2 teaspoons lemon juice), room temperature
  • 1 lemon, zested
  • 1 small orange, zested
  • 1 tablespoon vanilla extract or vanilla bean paste
  • 3 large eggs, room temperature
  • 1/2 cup granulated sugar
  • 1/3 cup neutral oil (I use grapeseed, sunflower, or avocado)

For the Lemon Honey Frosting


  • 2 sticks unsalted butter, softened
  • 3 tablespoons honey
  • 2 teaspoons vanilla bean paste or extract
  • 1 1/2 cups organic powdered sugar
  • 3 tablespoons heavy cream
  • 3/4 teaspoon kosher salt
  • 1 lemon, zested and juiced
  • 1 small orange, zested

For Decorating


  • Assorted fresh fruit, (berries, thinly sliced kumquats)
  • Edible flowers and herbs, (optional)

Make the Cupcakes


  • Step 1

    Cut out sheets of parchment paper sheets into 12 squares that are roughly 4.5 inches.

  • Step 2

    Use a round drinking glass roughly the same diameter as the cupcake pan wells, then mold each sheet over the glass, pressing tightly and pleating the long pieces to create seams. Unmold and invert—these are your cupcake liners!

  • Step 3

    Transfer each to the cupcake pan (or muffin tin).

  • Step 4

    Preheat the oven to 350°F.

  • Step 5

    Sift together the whole wheat flour, almond meal, baking powder, baking soda, and salt in a medium bowl.

  • Step 6

    Whisk the buttermilk, vanilla, lemon zest, and orange zest in a small bowl or a liquid measuring cup.

  • Step 7

    Beat the eggs and sugar in the bowl of an electric mixer fitted with the paddle attachment on medium speed until pale and fluffy, about 7 minutes.

  • Step 8

    Slowly stream in the oil and continue to beat the mixture for another 3 minutes.

  • Step 9

    Add half of the dry ingredients, mixing just until combined, then add half the buttermilk mixture.

  • Step 10

    Scrape down the sides of the bowl as necessary, then repeat with the remaining dry ingredients and buttermilk mixture. Stir batter by hand a few times to incorporate any ingredients stuck at the bottom of the bowl.

  • Step 11

    Divide the cupcake batter into parchment paper liners and bake for about 16-18 minutes. Allow cupcakes to cool completely in the pan before frosting.

For the Frosting

  • Step 1

    Meanwhile, make the frosting by beating together the butter, honey, and vanilla in the bowl of an electric mixer fitted with the paddle attachment until light and fluffy, about 5 minutes.

  • Step 2

    Add half of the powdered sugar and slowly stir to combine. Increase the speed to medium for just a short burst to lighten it up.

  • Step 3

    Add the heavy cream, kosher salt, lemon juice, lemon zest, and orange zest and beat on medium speed for about 3 minutes, until light and fluffy.

  • Step 4

    Remove about ½ cup frosting and place in a small heatproof bowl.

  • Step 5

    Microwave it for about 15 seconds on medium power, to heat the frosting but not melt it completely. (Alternatively, you can place the frosting in the warm oven for about 30 seconds.)

  • Step 6

    Add this warmed mixture back to the bowl and stir on medium speed until well combined. (This trick makes a super glossy and smooth frosting!)

  • Step 7

    Apply a dollop of frosting onto each cooled cupcake using a cookie scoop, then dig into the center at a 45-degree angle and a round motion with an offset spatula to create a little bowl in each mound of frosting.

  • Step 8

    Top with fruit and edible flowers and feel free to get creative with your arranging!

  • Step 9

    Serve the cupcakes at room temperature.

  • Step 10

    Store the cupcakes in an airtight container for up to 2 days, then transfer them to the refrigerator for up to 5 more days, bring them to room temperature before eating for the best results.