Lemon Meringue Cupcakes

How convenient it is to know how to cook and whip something up when you have a craving.

I used to divulge in lemon danishes – mmm the tangy lemon filling got me every time!

The inspiration for this Lemon Meringue Cupcake came from a cupcake shop in Toronto I went to a few years ago. I had a Strawberry Shortcake Cupcake, which was stuffed in the middle and topped with whipped cream. (While we’re on the subject, be sure to check out my Strawberry Shortcake Recipe)

I like cupcakes, cuz they are the perfect controlled portion size for dessert, so rather than making the traditional Lemon Meringue Pie, I opted for a stuffed cupcake version 🙂

You can grab the cupcake recipe from my Organic Vanilla Cupcakes and follow the instructions to make the lemon filling and the meringue itself.

This may seem difficult, but it is quite simple. If you know how to bake and use the proper tools, than you should be good to go!

Yields: 16 cupcakes (as per my Organic Vanilla Cupcakes recipe)

Lemon Filling Ingredients:
2 Egg Yolks at room temperature
⅓ cups Water
⅓ cups Cane Sugar
1 tbs Spelt Flour
2 tbs Arrowroot
Pinch of Sea Salt
1 tbs Coconut Oil
1 Lemons, juiced and zested

Meringue Ingredients:
2 egg whites
3 tbs Cane Sugar
½ tsp Vanilla Extract


Lemon Filling

  • In a medium sized pot, whisk Sugar, Spelt Flour, Arrowroot, and Sea Salt, mix ingredients together
  • Stir in Water, Lemon Juice and Lemon Zest until all ingredients are combined and there are no lumps
  • On medium-high heat, stir until lemon sugar mixture begins to boil
  • Add in Coconut Oil and stir
  • Gently separate Egg Yolks from Egg Whites, and set Egg Whites aside to use for Meringue
  • Place Egg Yolks in a small bowl, and whisk about half the lemon sugar mixture with the egg yolks
  • Whisk egg yolk mixture back into the remaining of the lemon sugar mixture in the pot
  • Bring to a boil and continue stirring
  • Let lemon filling cook for 15 minutes, until nice and thick. Be sure to stir!
  • Remove from heat and let sit until ready to use


  • In a medium sized glass or metal bowl, using an electric mixer, whip egg whites until they resemble a foamy texture
  • Add Vanilla Extract and continue mixing
  • Add sugar a tablespoon at a time, and continue to whip until stiff peaks form
    You can test this by lifting the beaters straight up from the egg whites, creating peaks on top of the egg whites
    Another method is to tilt the bowl, and ensure the mixture does not slide around

Creating the Lemon Meringue Cupcakes

    • Step 1) Bake cupcakes as per instructions if you are using my Organic Vanilla Cupcakess recipe
      * Small adjustment – do not use cupcake liners. Coat cupcake pan with butter or coconut oil

* Leave the oven on, as you will still need it

  • Step 2) While cupcakes are baking, prepare Lemon Filling
  • Step 3) While cupcakes are cooling, prepare Meringue
  • Step 4) Cut out a hole the size of a quarter, on top of the cupcakes, and gently remove enough cupcake to fill with Lemon Filling – be sure not to dig all the way to the bottom
  • Step 5) Fill the cupcake with Lemon Filling, using a teaspoon or piping bag
  • Step 6) Spoon Meringue on top of cupcake, creating a little peak (you may also use a piping bag for better control and consistency)
  • Step 7) Place cupcakes on a cookie sheet, and place on middle rack in oven. Bake for 10 minutes, or until Meringue is golden brown
  • Step 8) Let the Lemon Meringue Cupcakes cool for 30 minutes, than place in the fridge for an hour
    * It is important for this cooling process, to allow the lemon filling to solidify
  • Enjoy!


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