Lemon Cupcakes Made With Fresh Milled Flour

These lemon cupcakes made with fresh milled flour are the perfect blend of sweet and tangy. If you’re a fan of lemon desserts, this recipe is for you! But if you’re looking for a lemon cake instead, I will include those baking instructions below as well.

If you LOVE lemon, then you have to also try out my lemon bars, checkout my video HERE to see how.

How To Turn This Fresh Milled Flour Lemon Cupcake Recipe Into A Lemon Cake

1. Prepare the Batter: Use this same freshly milled flour lemon cupcake batter recipe.
2. Choose the Right Pan:
   • For a single-layer cake: Use a 9×13 baking pan, like a sheet cake style.
   • For a double-layer cake: Divide the batter between two 8-inch round cake pans.
3. Adjust the Baking Time:
   • A single-layer cake will take about 35-40 minutes.
   • For double-layer cakes, bake each layer for 25-30 minutes.
4. Cooling and Frosting– Let the cake cool in the pan for 15-20 minutes, then transfer to a wire rack to cool completely before frosting.
5. Optional Add-Ins: You can still incorporate any of the cupcake variations mentioned below (like blueberries, poppy seeds, or herbs) into the cake version for extra flavor!

Fun Variations & Add-Ins for Lemon Cupcakes

So, if you are looking to put a twist on these FMF lemon cupcakes, then try one of these creative variations to take them to the next level:

• Lemon Blueberry: Fold in ¾ cup fresh or frozen blueberries for bursts of juicy sweetness.
• Lemon Poppy Seed: Add 1-2 tablespoons of poppy seeds to the batter for a classic nutty crunch.
• Lemon Curd-Filled: Hollow a core out of the baked cupcakes and then fill with lemon curd for an extra citrusy surprise.
• Coconut Lemon: Stir ½ cup shredded coconut into the batter or sprinkle on top for a tropical touch.
• Raspberry Lemon Swirl: Add dollops of raspberry jam to the batter and lightly swirl for a tart, colorful swirl.
• Herbal Lemon: Infuse with 1 teaspoon of finely chopped fresh thyme, rosemary, or lavender for a sophisticated flavor boost.

These variations let you easily customize your cupcakes for any occasion or craving! So, let me know in the comments what your favorite flavor combination is!

Frosting Ideas To Top These Fresh Milled Flour Lemon Cupcakes

I topped these cupcakes with a simple Lemon & Vanilla Buttercream, but there are so many other delicious frosting options that would taste amazing on these. So here are some alternative frosting ideas:

• Lemon Cream Cheese Frosting:
  A tangy and creamy option that enhances the citrus flavor without being overly sweet. Beat together softened cream cheese, butter, powdered sugar, lemon zest, and a splash of lemon juice for a smooth, spreadable frosting.
• Lemon Glaze:
  If you prefer something lighter, a simple lemon glaze works beautifully. Mix powdered sugar with fresh lemon juice until smooth and pourable. Drizzle over the cupcakes for a glossy finish and extra tang.
• Raspberry Buttercream:
  For a fruity twist, blend fresh or freeze-dried raspberries into a buttercream base. The sweet-tart flavor of raspberries pairs wonderfully with lemon.
• Coconut Whipped Cream:
  For a tropical touch, whip coconut cream with a bit of powdered sugar and vanilla. This light and airy frosting adds a subtle sweetness that complements the lemon.
• Simple Dusting Of Powdered Sugar:
  These cupcakes are so full of flavor, that you can just use a simple dusting of powdered sugar over the top. This option is light, and not too sweet, which also lets the lemon shine through.

These frosting options will add the perfect finishing touch to your lemon cupcakes, whether you’re aiming for rich and decadent or light, simple, and refreshing!

Ingredients To Make Lemon Cupcakes With Fresh Milled Flour

Cupcake Batter Ingredients

• 3&1/4 cups fresh milled flour 376g (soft white wheat)
• 1/4 cup potato starch 32g (you can use cornstarch, tapioca starch, etc.)
• 4 tsp baking powder
• 1 tsp salt (if using unsalted butter)
• 1 cup softened butter 226g, not melted (2 sticks)
• 2 cups sugar 400g
• 4 large eggs room temperature
• 2/3 cup lemon juice (fresh squeezed is best) 160g
• 3 TBSP lemon zest (from about 2-3 lemons)
• 1 TBSP vanilla extract
• 1 cup whole milk 240g (room temperature)

Lemon & Vanilla Bean Buttercream Frosting Ingredients

• 1 vanilla bean sliced longwise, and scrape out the vanilla beans
• 1/2 tsp Vanilla Extract
• 1 TBSP lemon zest (from about 1 lemon)
• 1&1/2 cup softened butter 340g Not Melted (3 Sticks)
• 3 cups powdered sugar 360g to taste
• pinch of salt if using unsalted butter
• 1-2 TBSP whole milk to thin if needed 15-30g can use heavy cream or half and half also

Instructions To Make Lemon Cupcakes With Fresh Milled Flour

Make The Cupcake Batter

1. Firstly, mill the flour. I like to use all soft white wheat.
2. Then, add the starch, baking powder, and salt (if using unsalted butter) to the flour, and stir to combine. Set aside.
3. In a stand mixer, add room temperature butter and sugar. Cream together for 3-5 minutes until it becomes lighter in color, and increases in volume. Also, make sure to scrape the sides down as needed for even mixing.
4. Add eggs one at a time, mixing a little between each egg. Then, after all the eggs are incorporated, beat until mixture becomes fluffy (about 1-2 minutes more.)
5. Then, add the vanilla extract, lemon juice, and lemon zest. Mix until well combined.
6. Now, it is time to add in your flour mixture. Slowly mix in half the flour without overmixing.
7. Then, add in the whole milk, mix in just a little.
8. Lastly, add in the rest of the flour, and fold in with a spatula just until there is no dry flour mixture left. Don’t overmix it will deflate all the air you put in the cake, and make it tough.

Prepare For Baking

1. Preheat the oven to 350*F.
2. Let the lemon cupcake batter sit and allow the fresh milled flour to start absorbing all the liquid while the oven preheats. (15 mins or so.)
3. Line the cupcake tins with liners.
4. Fill each cupcake liner with about 1/4 cup of batter . It should fill the liner about 2/3rds of the way full. This will allow room for the cupcakes to rise.
5. Bake for 18-22 minutes. This baking time will vary, but make sure to check with a toothpick for doneness. Pull them out as soon as the toothpick is clean. Over baking will cause dry and/or crumbly cupcakes.
6. Allow the cupcakes to cook in the pan for about 10 minutes.
7. Then, remove them from the pan, and onto a cooling wire rack to finish cooling the rest of the way.
8. Make sure they are completely cooled before frosting the cupcakes.

Make The Lemon and Vanilla Bean Buttercream

1. To make the lemon & vanilla bean buttercream, in a clean bowl in a stand mixer, add room temperature butter, salt, powdered sugar, vanilla extract, lemon zest, and vanilla beans from the pod. (but, not the pod)
2. Then, mix on low speed for a few minutes until the ingredients are incorporated. Once combined, then turn up the speed to medium-high/high and mix until light and fluffy. Scrape the sides of the bowl as needed for even mixing.
3. Adjust the sweetness by adding more or less powdered sugar. Then, slightly thin the buttercream buy adding whole milk a little at a time. Once, the buttercream is the sweetness, and thickness you prefer, it is done. Don’t frost the cupcakes until they have completely cooled.
4. Lastly, enjoy!

How To Store Fresh Milled Flour Lemon Cupcakes

To store these fresh milled flour lemon cupcakes, cover and let sit at room temperature for up to 2 days. But, I recommend freezing these for long term storage. I like to set the on a baking sheet and place in the freezer for about 2 hours, then once they are frozen solid, place them in a a freezer bag. They will last in the freezer for up to 3 months. (I freeze them with the frosting on and all!) To thaw, just place at room temperature for 1-2 hours.

Check Out Some Of My Other Recipes

Lemon Bars

Pizza Dough

Cut-Out Cookies

Vanilla Cupcakes

Chocolate Cake

Pancakes

Cheese Crackers

Garlic Cheese Biscuits

Dinner Rolls

Fresh Milled Flour Recipe Index

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Fresh Milled Flour Lemon Cupcakes Printable Recipe

Lemon Cupcakes Made With Fresh Milled Flour

These lemon cupcakes made with fresh milled flour are the perfect blend of sweet and tangy. If you’re a fan of lemon desserts, this recipe is for you! But if you’re looking for a lemon cake instead, I will include those baking instructions below as well.

Print Recipe Pin Recipe

Prep Time 30 minutes mins

Cook Time 18 minutes mins

Cooling Time 1 hour hr

Total Time 1 hour hr 48 minutes mins

Course Dessert

Cuisine American

Servings 24 cupcakes

Ingredients

  

Cupcake Batter Ingredients

• 3&1/4 cups fresh milled flour 380g soft white wheat
• 1/4 cup potato starch 32g you can use cornstarch, tapioca starch, etc.
• 4 tsp baking powder
• 1 tsp salt if using unsalted butter
• 1 cup softened butter 226g not melted (2 sticks)
• 2 cups sugar 400g
• 4 large eggs room temperature
• 2/3 cup lemon juice 160g fresh squeezed is best
• 3 TBSP lemon zest from about 2-3 lemons
• 1 TBSP vanilla extract
• 1 cup whole milk 240g room temperature

Lemon & Vanilla Bean Buttercream Frosting Ingredients

• 1 vanilla bean sliced longwise and scrape out the vanilla beans
• 1/2 tsp Vanilla Extract
• 1 TBSP lemon zest from about 1 lemon
• 1&1/2 cup softened butter 340g 3 Sticks (Not Melted)
• 3 cups powdered sugar 360g to taste
• 1 pinch salt if using unsalted butter
• 1-2 TBSP whole milk to thin if needed 15-30g can use heavy cream or half and half also

Instructions

 

Make The Cupcake Batter

• Firstly, mill the flour. I like to use all soft white wheat.
• Then, add the starch, baking powder, and salt (if using unsalted butter) to the flour, and stir to combine. Set aside.
• In a stand mixer, add room temperature butter and sugar. Cream together for 3-5 minutes until it becomes lighter in color, and increases in volume. Also, make sure to scrape the sides down as needed for even mixing.
• Add eggs one at a time, mixing a little between each egg. Then, after all the eggs are incorporated, beat until mixture becomes fluffy (about 1-2 minutes more.)
• Then, add the vanilla extract, lemon juice, and lemon zest. Mix until well combined.
  
• Now, it is time to add in your flour mixture. Slowly mix in half the flour without overmixing.
• Then, add in the whole milk, mix in just a little.
• Lastly, add in the rest of the flour, and fold in with a spatula just until there is no dry flour mixture left. Don’t overmix it will deflate all the air you put in the cake, and make it tough.
• Preheat the oven to 350*F.
• Let the lemon cupcake batter sit and allow the fresh milled flour to start absorbing all the liquid while the oven preheats. (15 mins or so.)
• Line the cupcake tins with liners.
• Fill each cupcake liner with about 1/4 cup of batter . It should fill the liner about 2/3rds of the way full. This will allow room for the cupcakes to rise.
• Bake for 18-22 minutes. This baking time will vary, but make sure to check with a toothpick for doneness. Pull them out as soon as the toothpick is clean. Over baking will cause dry and/or crumbly cupcakes.
• Allow the cupcakes to cook in the pan for about 10 minutes.
• Then, remove them from the pan, and onto a cooling wire rack to finish cooling the rest of the way.
• Make sure they are completely cooled before frosting the cupcakes.
  

Make The Lemon and Vanilla Bean Buttercream

• To make the lemon & vanilla bean buttercream, in a clean bowl in a stand mixer, add room temperature butter, salt, powdered sugar, vanilla extract, lemon zest, and vanilla beans from the pod. (but, not the pod)
• Then, mix on low speed for a few minutes until the ingredients are incorporated. Once combined, then turn up the speed to medium-high/high and mix until light and fluffy. Scrape the sides of the bowl as needed for even mixing.
• Adjust the sweetness by adding more or less powdered sugar. Then, slightly thin the buttercream buy adding whole milk a little at a time. Once, the buttercream is the sweetness, and thickness you prefer, it is done. Don’t frost the cupcakes until they have completely cooled.
• Enjoy!
  

Notes

*To store these fresh milled flour lemon cupcakes, cover and let sit at room temperature for up to 2 days. But, I recommend freezing these for long term storage. I like to set the on a baking sheet and place in the freezer for about 2 hours, then once they are frozen solid, place them in a a freezer bag. They will last in the freezer for up to 3 months. (I freeze them with the frosting on and all!) To thaw, just place at room temperature for 1-2 hours.

*To make this into a cake instead of cupcakes, see my blog post for baking instructions.

Keyword fmf lemon cupcakes, fresh milled flour lemon cake, lemon cake, lemon cupcakes

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