Organic Cupcakes Recipe from Scratch

Last Updated on May 7, 2023 by Ellen Christian

Looking for a recipe for organic cupcakes? Try this natural cupcake recipe that is both easy and delicious. It’s a family favorite recipe.

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organic cupcake recipe from scratch

Organic Cupcake Recipe from Scratch

While I very rarely eat baked goods, some occasions just call for cake or cupcakes.  Marty’s birthday is coming up soon and his one request was cupcakes.  

Normally, I would head to the grocery store for a box of cake mix and go from there.  Since I started looking at ingredients, I knew this wasn’t going to work for us any longer. 

 Did you know that most cake mixes have corn syrup which is most likely from GMO corn and a variety of artificial flavors and food dyes? Since it’s fairly easy to make an organic cupcake recipe from scratch, I decided I would do that instead.

Check out the organic cupcakes recipe at the end of the post.

I purchase our organic and local food from our local food coop. Our grocery stores carry a very poor selection of organic products.

If you live in a larger town or city, you may have better luck than I do.  Whenever possible, I buy local and organic.

frosted cupcakes on a cooling rack

Healthy cupcake recipes

Yes, it really is possible to find relatively healthy cupcake recipes. Everything in moderation is acceptable.

So, while one or two organic cupcakes is not a problem, eating a dozen would not be a good idea.

You might want to check out my natural fruity tie-dye Easter cupcakes that are made with natural coloring.

baked goods on a cooling rack

I used organic sucanat as a sweetener in this organic cupcakes recipe. Sucunat is pure dried sugar cane juice. You can get it here.

Unlike traditional white sugar, sucanat is not refined and has the molasses mineral content that is lost in the refining process.  

healthy natural sweeteners

It is more similar to brown sugar however traditional brown sugar is just white sugar with a bit of molasses added back to it.  Organic sucanat has the mineral content that is missing in traditional sugars which makes it a healthier choice to bake with in my opinion.

You can use sucanat as a replacement for traditional white sugar without adjusting the measurements in most recipes. You may want to check out these healthy baking substitutes for allergy-friendly cooking.

fluffy vanilla cupcakes

If you’re looking for a fluffy vanilla cupcakes recipe, this one is probably a bit denser than the traditional fluffy cupcake. Here are some cupcake baking tips that may help you achieve the fluffy level that you want.

Generally speaking, the more you sift the flour the fluffier the final cupcake will be. It cannot hurt to try and see what results you get when you sift versus when you don’t.

Vegan cupcakes

If you’re looking for vegan cupcakes, you might want to try a few substitutions in this organic cupcakes recipe and see how it turns out. The recipe does call for milk, eggs, and butter so you would have to experiment a little bit.

Or, you can try these vegan vanilla cupcakes from Food Network.

cupcakes with natural pink strawberry frosting

Strawberry organic cupcakes

If you’re looking for an organic cupcakes recipe that has just a hint of strawberry flavor, why not try these organic cupcakes topped with my natural frosting recipe. It uses fresh strawberries so it has a touch of strawberry flavor and a natural light pink color.

muffin liners

So, you may have noticed that I love using paper cupcake liners. For parties, they are perfect because they keep fingers off the cupcake itself when handing things out.

But, at home, we generally use reusable silicone cupcake liners to reduce paper waste. I love these reusable silicone baking cups because the cupcakes or muffins just pop right out.


organic cupcake recipe from scratch

More healthy dessert recipes

If you enjoy healthy dessert recipes, why not try these healthy peanut butter banana bars. They make a great after school treat for the kids.

Or, if you want a holiday treat, check out these healthy Christmas treats or this healthy Valentine’s Day dessert. Or, these Paleo pumpkin bars are great for Thanksgiving.

Now, if you are planning on serving these organic cupcakes at a party or an event, you really need to serve them on a cupcake tree. It is so much easier than trying to fit them all on a plate.

This one is collapsible and has a cover in case you need to take them with you to a party. Or, if you want to take a cupcake with you for lunch, try this cute cupcake holder. It will help keep it safe until you want to eat it.

More recipes

Yield: 18

Organic Cupcakes Recipe from Scratch Organic Frosting Recipe

organic cupcake recipe from scratch

Looking for a recipe for organic cupcakes? Try this natural cupcake recipe that is both easy and delicious. It's a family favorite.

Prep Time 15 minutes
Cook Time 17 minutes
Additional Time 15 minutes
Total Time 47 minutes


  • 1 cup organic, raw local milk
  • 6 farm fresh egg whites (organic)
  • 1 tsp pure organic vanilla extract
  • 2 1/4 cups organic white flour (unbleached)
  • 1 3/4 cups Wholesome Sweeteners Organic Sucanat
  • 4 tsp baking powder
  • 1 tsp sea salt
  • 6 ounces organic butter (1 1/2 sticks), softened & cut up
  • 8 ounces (2 sticks) of organic unsalted butter, softened
  • 4 cups Wholesome Sweeteners Organic Powdered Sugar
  • 1 tbsp pure organic vanilla extract
  • 2 tbsp organic raw milk (or pasteurized if you cannot find raw)


  1. Preheat oven to 350F. Line muffin pans with cupcake liners if you use them or grease muffin pans to prevent sticking.
  2. Put milk, egg whites, and vanilla in bowl and beat with fork.
  3. Mix flour, sugar, baking powder and salt with electric beater on low. Add pieces of the butter slowly until it looks like crumbs.
  4. Reserve 1/2 cup of milk mixture and add the rest to the dry ingredients beating for one minute. Add the rest of the milk and beat until combined.
  5. Pour batter into muffin cups about 3/4 full.
  6. Bake 15 -17 minutes or until they test done.
  7. Cool completely before frosting them.
  8. Beat the butter, powdered sugar, vanilla and milk with an electric beater on low until moistened.
  9. Beat on medium until creamy and fluffy.
  10. Pipe or spread on completely cooled cupcakes.

Nutrition Information:



Serving Size:


Amount Per Serving: Calories: 327Total Fat: 18gSaturated Fat: 11gTrans Fat: 0gUnsaturated Fat: 6gCholesterol: 49mgSodium: 327mgCarbohydrates: 38gFiber: 0gSugar: 24gProtein: 4g

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92 thoughts on “Organic Cupcakes Recipe from Scratch”

  1. We would just love this cupcake! Hope you are having a great week and thanks so much for sharing this awesome recipe with Full Plate Thursday. Come Back Soon! Miz Helen
  2. I learned that the Fairtrade premiums from the sale of Organic honey in Mexico are used partially to build schools and healthcare centers. Very cool.
  3. I learned they have alot of great ideas about how to use their products as well as a featured chef section--maybe you'll be featured there next :)
  4. I've never tried any of their products but it looks like they have a great variety. I checked out their page and learned that it isn't a page to visit when you're hungry or have a sweet tooth because now I want to eat something sweet. The recipes look awesome! I'm a fan of Stevia so it was nice to see they offer it in bulk as well as in packets.
  5. I grew up on the NH seascoast. While it's not exactly rural, we did eat pretty much everything organic and most of our veggies came straight out of the garden. Eating organic in South Florida is SO expensive! People are into the gimmick side of healthy living down here and it's been really hard to find products "worth" spending the money on. Wholesome Sweetners looks like an honest company that has my "kind" of values! Your blog makes me miss home so much!
  6. I learned that they support farmers through Fair Trade - I love this company.  I called this company once since I couldn't find their products where I lived and got a great response.  Check out my blog post about it:
  7. I learned that bagasse is used sugar cane and it is used as fuel for the boilers that power the sugar mills and surrounding villages.
  8. I learned that on the farms in Indonesia they, and the surrounding area, are powered by fuel made from sugar cane. / danabeeman(at)gmail(dot)com
  9. I learned that the company "Wholesome Sweeteners" supports fair trade, sustainability, and is committed to Non-GMO growing practices!  Hooray!
  10. I learned about their blue agave sweetener which I've been curious about. It's neat that it is a low glycemic sweetner and since it is sweeter to the tongue you use less than normal.
  11. The fact that they have been in business since 2001 and they make a commitment to make the best tasting sweeteners leave the smallest footprint to the earth as possible.
  12. Ellen is a pretty blonde lady that does things right. You're busy being a mom of 2 teens and love cooking, crafting, family, & the country life. Everything as it was when I was young. Wholesome Sweeteners has great proudcts, which I use a lot of. The organic sugars can all be found in my kitchen, in various amounts. I'd love refills. They're a great company, so Ellen is a great fit with them.
  13. I learned that Sucanat is made from 100% certified organic sugar cane. and contains all of the cane's natural molasses, So cool. 
  14. I learned that Wholesome Sweeteners holds fast to a "Fair Trade, Not Aid" philosophy.  I think this is wonderful for farmers and we do try to buy fair trade products often.
  15. I visited their site and was amazed at the different kinds of sugar that they have available. I didn't realize there were so many.
  16. I visited their website and read about their sustainability...I found out that they harvest from organic coconut palm trees that produce for 25-40 years and are not cut down. This is so interesting and important...
  17. Marilu Henner, the actress is author of seven successful healthy lifestyle and cookbooks! Learn something new every day ;)
  18. What a wonderful site! On top of having great products, there are sooo many recipes I want to try that use sweeteners I have or want to try!
  19. I learned that they are the leading provider of sustainable, environmentally and ethically responsible sweeteners in the USA
  20. I think my eye balls just popped out of my head and I drooled on my keyboard! LOL Sad to say but I'm sweets driven and a good, organic cupcake is hard to find. These look absolutely amazing and I'm super impressed by the natural aspect of them :) I learned that they are Non-GMO verified which is one thing my family and I look for in our food choices! Thank you for the great giveaway AND the fantastic cupcake recipe.
  21. I haven't looked for this brand before. My stores are always hit and miss in the organic section. I went to their site and learned that they support Fair Trade. 
  22. I always learn something great when I visit your blog. I have been incorporating more organic foods into my diet, and will definitely be seeking out some of these products.
  23. I love Wholesome Sweeteners and love that they offer Raw Honey! Sucanat is an adjustment at first but we really enjoy the rich flavor it gives.
  24. Wow, those cupcakes look scrumptious! What a fantastic idea. I learned a little about Organic Sucanat today. Thanks for sharing this, I am very interested in trying it out.. asap! Thank you!
  25. You are one busy baker! I haven't seen these products, but definitely interested. Sounds like a better option for sure. The cupcakes look DELICIOUS!!
  26. I love baking from scratch. I truly believe the flavors are so much better. Going to add this recipe to the "Must Try" list! They look amazing.
  27. We LOVE Wholesome Sweeteners. I use their brown and white sugar. Didn’t know they had honey. I have to try their other products!(Let me start with this yum recipe!!)
  28. Okay, so my confession is that I have never baked anything from scratch... ha... Thanks so much for this recipe, it looks amazing. 
  29. I like that they support fair trade, I've used their coconut palm sugar before and loved it, I'd love to try their different types of organic sugar for making my water kefir.
  30. Oh, I think this would be a fantastic recipe to create! i love the use of Sucanat! I want to give some of that a try. I'm always looking for healthier sweetener options.  I love the brand too! I purchase a lot of Wholesome sweeteners from our store, but I haven't seen some of these sweeteners. I want to give them all a try. I love that they have recipes on their website, for more ideas of how to use their sweeteners. 
  31. These look awesome, Ellen!! I LOVE Wholesome Sweeteners.  Fabulous company, and fabulous products.  I was introduced to them at a conference last year and love them still!
  32. Your cupcakes look delicious and I love that they are organic! I really need to start concentrating on making more healthy versions of my favorite baked goods!
  33. I have seen there line of products at our local ORganic Cupboard. I personally haven't tried it yet, but might have to. 
  34. This is a great simple recipe, I didn't know it could be so easy! I have to admit, 'making organic' kinda freaks me out a bit!
  35. I have a bunch of their products that I got at a conference. I guess I need to start using them more often if I can make treats like this!

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