Vegan Brownie Cupcakes

(from 4 reviews)
Vegan Brownie Cupcakes

I had mentioned about vegan brownie cupcakes in my previous post and here I’m with the recipe. Actually 2 weeks back it was my son’s turn to provide snacks for his classmates in preschool and I was wondering what to bake from the humungous collection of eggless recipes I have now. Since I’m hosting this event, I decided to bake something using flax seed meal. I wanted to bake something simple, which appeals children and that can be easily packed. I had borrowed “The Joy of Vegan Baking” book from the library and this brownie recipe (the author has actually adapted the recipe from Sinfully Vegan) caught my eye. Do you know the reason? It does not have any added fat like butter/oil etc. Applesauce is replaced for fat in the recipe. I’m aware of the fact that unsweetened applesauce recipe can be used as an egg substitute as well as a fat substitute, but I have tried neither. So I was determined to try this recipe because I will be baking something healthy and who doesn’t like brownies, leave alone preschoolers.

If you have baked brownies before you would know that it takes a long time to cool and then you have to cut it. I wanted to bake 35 brownies and the recipe mentioned that it would yield 8-9 brownies, so I would have to bake 4-5 batches, take into account the cooling time, packing etc, which would consume a considerable amount of time. Then only I remembered what I had read a long time back in a magazine. One of the readers had mentioned that she baked brownies in a muffin tin and they came out very well. I decided to try it and I’m so glad that I tried it because it’s such a wonderful/neat idea. I think I’ll be baking brownies only in a muffin tin henceforth. Moreover the serving size is also increased to 12 from 8, using a muffin pan instead of a regular baking dish. So I had to bake only 3 batches.


Vegan Brownie Cupcakes Recipe

Prep TimeCook TimeMakes
15 Mins23 Mins + Cooling Mins12 Cupcakes
Vegan Brownie Cupcakes
4.5 from 4 reviews
A very simple recipe to bake healthy vegan brownies. But let me assure that it tastes like the regular brownies which are loaded with fat.
  • 1 And 1/2 Cups Granulated Sugar Or Sweetener (I Used Regular Sugar)
  • 3/4 Cup Unsweetened Applesauce (I Used Nature’s Promise Organic Applesauce)
  • 2 Tablespoons Water
  • 2 Teaspoons Flax Seed Powder
  • 1/2 Cup Water
  • 2 Teaspoons Vanilla Extract (I Used Trader Joes Pure Vanilla Flavor Alcohol Free)
  • 1 And 1/3 Cups All Purpose Flour
  • 3/4 Cup Cocoa (I Used Hershey’s)
  • 1 Cup Vegan Chocolate Chips (But I Used The Regular Nestle Ones)
  • 1 Cup Optional Chopped Walnuts (I Omitted)
  • 3/4 Teaspoon Baking Powder
  • 1/4 Teaspoon Salt
  1. Preheat oven to 350F/180C for 15 minutes.
  2. Coat an 8×8 inch square baking dish with nonstick cooking spray. If you choose to bake brownie cupcakes, line a 12 muffin tin with muffin liners or coat with nonstick cooking spray itself.
  3. In a medium size bowl, stir together sugar, applesauce and 2 tablespoons water.
  4. Either mix flax seed meal with 1/2 cup water in a small cup or blend it in a blender.
  5. Add the flax seed mixture and vanilla to the applesauce mixture and combine well.
  6. In another small bowl, combine flour, cocoa, baking powder, salt, chocolate chips and walnuts (if using).
  7. Add the wet ingredients to the flour mixture.
  8. Stir just to combine, do not overmix.
  9. Pour into prepare pan. If using a muffin tin, fill each mould 3/4ths full. The given measurement is perfect for 12 muffins, so divide the batter accordingly, which is around 3-4 tablespoons of batter in each cup.
  10. The time given in the original recipe for baking in a brownie pan is 40 minutes for chewy brownies and 45-47 minutes for cake like brownies. But since I used a muffin tin to bake brownies, mine was done exactly at 23 minutes.
  11. Once the cupcakes are out of the oven, leave it in the tin for 2 minutes and then transfer to a wire cooling rack for the brownie cupcakes to cool completely.
  1. As for the taste, it was AWESOME. You can never guess that these are healthy brownies. They were so moist. I was not able to get the feedback from the children, but one of the teachers told me that it tasted very good and the children really enjoyed it.
My Notes:
  1. While buying applesauce, check thoroughly the ingredients list. Some brands have very large amount of high fructose corn syrup, which increases the sugar content to 25gms per serving. I think unsweetened applesauce is available only in organic brands. The Nature’s Promise brand is made only with organic apples and water. It does not have any additional sweeteners, so 1/2 cup serving has only 9gms sugar which is actually from the apples.
  2. I used muffin liners to line the tin, which made the clean up also very easy. Another advantage of using muffin tins is, they cool in no time.
  3. These brownie cupcakes taste better the next day of baking.

Nutrition Facts
Servings: 12
Per Serving% Daily Value*
Calories 313
Total Fat 11.9g18%
Saturated Fat 3.7g19%
Trans Fat 0g
Cholesterol 3mg1%
Sodium 64mg3%
Potassium 300mg9%
Total Carb 50.4g17%
Dietary Fiber 3.9g15%
Sugars 34.1g
Protein 6.3g
Vitamin A 1% – Vitamin C 1%
Calcium 6% – Iron 13%
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Tried this recipe? Click on stars to rate:


  1. Linda Smock

    You never mentioned if the kids liked them ??? Just wondering?

    • Madhuram

      Yes they did 🙂

  2. Mansi

    whats the best way to store cup cakes? should we refrigerate or room temperature is ohk?

    • Madhuram

      Room temperature for a couple of days is ok. But if it has fruit puree in it or you want to have it after a couple of days storing it in the fridge or freezer is a better idea.

  3. Kamala Raghunath

    The texture of the cupcakes came out well. However, the cupcakes were not sweet enough. Perhaps we have to increase the amount of sugar? Did you ask for unsweetened apple sauce? What do you suggest?

    • Madhuram

      Mmm…we found the sweetness ok. Yes it is unsweetened applesauce. You can try increasing the quantity of sugar and see how it turns out.

  4. Nidhi

    I made more than 60 cupcakes using this recipe for my nephew birthday celebration at school. I didn’t grease the liners so it was sticky on day one but next day when we distributed it was perfect. Thank you for the recipe

    • Madhuram

      You’re welcome Nidhi. Yes, cupcakes do come out easily off the wrapper the next day.

  5. Jeya

    Hi Madhuram,

    Is there no oil/butter in this recipe?. I dont have applesauce. what can i use instead? I am thinking of baking it today. Pls let me know.

    • Madhuram

      The purpose of the recipe is to make it fat free and that’s why applesauce is used. If you don’t have it, then you can try other brownie recipes I have which either use oil or butter and bake it in muffin tins.

  6. On a Quest for Great Vegan Brownies

    These brownie cupcakes have the best overall taste and texture experience of any vegan brownies I’ve yet made, and I’ve been searching for quite a while now. I also love how they’re low-fat, virtually no-fat. My only critique is that they stuck to the cupcake wrappers a lot; I couldn’t pull the wrappers off without tearing into the cupcake. I think I overcooked mine a little, so that might have something to do with it. I’ll definitely be trying to make these again, though maybe without the cupcake paper.

    • Madhuram

      Low fat muffins/cupcakes do tend to stick to the paper liners. So you have got to spray the liners generously with non-stick cooking spray or wait until next day for the wrappers to come off easily. But I’m glad that you liked the taste and texture.

  7. Tiffani

    These will be a favorite of mine I think forever. My bf doesnt care for cocoa so I make these whenever I have to have my private chocolate fix. So healthy and delicious. If I were a cupcake this is what I’d be! 🙂

    • Madhuram

      Thanks a lot Tiffani. Hope you can rate the recipe when you find time.

  8. nk

    If I am substituting whole wheat pastry flour for all purpose, is it the same quantity?

    • Madhuram

      Yes, use the same quantity.

  9. nk

    Can I use whole wheat flour for this recipe? If so, how much?

    • Madhuram

      If you haven’t baked with whole wheat flour or used to the taste of whole wheat flour in baked goods, I would suggest using half whole wheat flour and half all purpose flour. Plain whole wheat flour “DOES NOT” taste good in all recipes and especially in cake recipes. If you still want to use it, try finding white whole wheat flour or whole wheat pastry flour. Bulk Barn has whole wheat pastry flour (its called soft wheat flour) or try the organic aisles of grocery stores/Whole Foods etc. Also you should be careful while preparing batter with whole wheat flour because over mixing whill toughen the cake/cookies.

  10. rani

    hi how are you?i am so loving your recipes. it’s very very good thank you very much for that. i have one Question for you one my friend is wondering if your can please show us how to make a cheesecake. she loves cheesecake bu, the thing is that it has a eggs in it so she can’t eat.

    I’m fine Rani, thank you. Cheesecake has been in my list for quite sometime now but couldn’t get to it until now. I’ll see what I can do Rani.

  11. Anusha Ravichandran

    Hi Madhu..

    If I add flax seeds powder 2 tsp should I still add the 1/2 cup of water? Also will the consistency of the dough be the same if its cupcake or brownie?

    Anusha the 2 tsp of flax seed powder is to replace 2 eggs and 1/4 cup of water for each egg. The consistency will remain the same but if you bake it as brownies it is going to take twice as much as time as baking them as cupcakes; about 35-40 minutes minimum.

  12. Carole


    I would love to make these for my daughter’s birthday but she cannot have gluten, so wheat flour is out of the question and as well she cannot have spelt flour or barley flour. What kind of flour can I use?? HELP!!

    Hi Carole, I do not bake gluten free so I have very limited knowledge about this. I think I have seen some gluten free flour mix in a bulk store or somewhere. Have you tried that before? I googled and found something. See if it is of any use.