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    Home » cupcakes & muffins

    Published: Mar 29, 2020 • Modified: Apr 28, 2022 • This site generates income via ads and may contain affiliate links. See my privacy policy linked in the footer.

    Simple and Delicious Black Bottom Cupcakes

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    Pinterest image of Black Bottom Cupcakes from BeyondtheButter.com | All Images © Beyond the Butter®

    These Simple and Delicious Black Bottom Cupcakes are marbled masterpieces that will melt in your mouth the minute you take a bite! They are rich, chocolatey, super moist, and filled with the creamiest chocolate chip cream cheese filling ever!

    Overhead image of black bottom cupcakes on gray background | All Images © Beyond the Butter™
    Overhead image of black bottom cupcakes randomly placed on gray background | All Images © Beyond the Butter™
    Close up angled image of black bottom cupcakes randomly placed on gray background | All Images © Beyond the Butter™
    Overhead image of black bottom cupcakes randomly placed with a half sliced cupcake and knife on gray background | All Images © Beyond the Butter™

    Table of Contents

    • Behind the Recipe
    • How to Make Black Bottom Cupcakes
      • Cream Cheese Filling
      • Chocolate Cupcakes
    • Helpful Recipe Tips
    • How Do I Fix Lumpy Cream Cheese?
    • More Cupcake and Muffin Recipes!
    • Need a Small Batch Version?

    Behind the Recipe

    I can remember growing up and being all kinds of excited when one of my Aunts would make these gooey chocolate black bottom cupcakes for a family gathering. When I'd see them sitting on the kitchen counter, my eyes would light up! They were one of my favorite treats as a kid and they still are as an adult too!

    Overhead closeup image of black bottom cupcakes randomly placed on gray background | All Images © Beyond the Butter™
    Close up angled image of black bottom cupcakes randomly placed on gold serving plate on a gray background | All Images © Beyond the Butter™

    How to Make Black Bottom Cupcakes

    This simple and delicious black bottom cupcake recipe is broken out into two parts—the cream cheese filling, which you make first, and the chocolate cupcakes.

    Cream Cheese Filling

    ingredients needed: cream cheese, granulated sugar, an egg, chocolate chips

    recommended baking tools: medium-size mixing bowl (preferably glass) and hand-held mixer or stand mixer fitted with the paddle attachment, spatula

    Before starting (and this is important!), your cream cheese needs to be softened and at room temperature. The egg should be at room temperature as well. Beat the cream cheese for 2-3 minutes on medium-high speed until it's nice and smooth. Add in the sugar, then the egg. Add in the chocolate chips last using a spatula.

    Chocolate Cupcakes

    ingredients needed: all-purpose flour, unsweetened cocoa powder, baking soda, granulated sugar, eggs, vegetable oil, water, apple cider vinegar, and vanilla extract

    recommended baking tools: large-size mixing bowl and hand-held mixer or stand mixer fitted with the paddle attachment, spatula, cookie scoop, 2 cupcake tins, cupcake liners

    The chocolate cupcakes are the second part of this recipe. When mixed together, the batter will be on the runnier side. This is because of using the oil which makes the cake super moist. I suggest using a cookie scoop to place the batter into each cupcake liner. It will make things easier for you and it will be less messy.

    I whisked the dry ingredients together, then added the wet ingredients. Keep your hand-held or stand mixer speed on low as you add in the wet ingredients to avoid any splatter.

    Close up overhead image of cupcake tin full of freshly made simple and delicious black bottom cupcakes on gray background | All Images © Beyond the Butter™
    Angled image of black bottom cupcakes randomly placed on gray background | All Images © Beyond the Butter™

    Helpful Recipe Tips

    • Your eggs should be at room temperature before starting.
    • The cream cheese should be softened and at room temperature. If it's still even the slightest bit cold, it will leave small lumps in the filling and look like cottage cheese.
    • Fill the cupcake liners only half way full to leave room for the dollop of cream cheese filling.
    • This simple and delicious black bottom cupcakes recipe can easily be made in a 13" x 9" x 1" baking pan. Bake at 350°F for 45 minutes.
    Overhead closeup image of black bottom cupcakes randomly placed on gray background | All Images © Beyond the Butter™
    Overhead image of black bottom cupcakes randomly placed on gold serving plate on a gray background | All Images © Beyond the Butter™

    How Do I Fix Lumpy Cream Cheese?

    Here are a few tips to try if you run into the dreaded lumpy cream cheese.

    Microwave it. In a microwaveable bowl add the cream cheese mixture and heat it for only 10-15 seconds at a time to help melt the cream cheese. Avoid heating it for longer amounts of time because you don't want to cook the egg in the process. Whisk the mixture again until the lumps have dissolved.

    Try the food processor. Place the cream cheese mixture into a food processor and pulse for a few seconds.

    Start over. The warming method has worked for me in the past, but sometimes nothing seems to fix it, in which case I would say to just start over again. This time with room temperature, softened cream cheese, and a room temperature egg.

    Overhead image of black bottom cupcakes randomly placed on gray background | All Images © Beyond the Butter™
    Close up angled image of black bottom cupcakes randomly placed with a half sliced cupcake on gray background | All Images © Beyond the Butter™

    More Cupcake and Muffin Recipes!

    • Super Moist Carrot Cake Cupcakes
    • Lemon Blueberry Streusel Muffins
    • Chocolate Zucchini Cake with Chocolate Chips (can be made as cupcakes)
    • Bakery Style Chocolate Chip Muffins
    • Devil's Food Cupcakes with Peanut Butter Frosting

    Need a Small Batch Version?

    If you're looking for a scaled-down version of this black bottom cupcakes recipe, check out my Small Batch Black Bottom Cupcakes! The recipe yields 6 cupcakes using the standard cupcake liners or more if you go with my favorite Wilton wave cupcake liners. They're just as good as the original, but perfect for a smaller crowd with no leftovers!

    Close up angled image of black bottom cupcakes randomly placed on gray background | All Images © Beyond the Butter™

    Simple and Delicious Black Bottom Cupcakes

    Author: Jennifer
    These Simple and Delicious Black Bottom Cupcakes are marbled masterpieces that will melt in your mouth the minute you take a bite! They are rich, chocolatey, super moist, and filled with the creamiest chocolate chip cream cheese filling ever!
    5 from 11 votes
    Print Recipe Pin Recipe
    Prep Time 30 minutes
    Cook Time 25 minutes
    Total Time 55 minutes
    Course Cupcakes
    Cuisine Dessert
    Servings 30 servings

    Ingredients
     

    chocolate chip cream cheese filling

    • 8 oz Cream Cheese (softened and at room temperature)
    • ½ cup Granulated Sugar
    • 1 Large Egg (room temperature)
    • 6 oz Semi-Sweet Chocolate Chips

    chocolate cupcakes

    • 3 cups All-purpose Flour
    • ½ cup Unsweetened Cocoa Powder
    • 2 teaspoon Baking Soda
    • 2 cups Granulated Sugar
    • 2 Large Eggs (room temperature)
    • ⅔ cup Vegetable Oil
    • 2 cups Water
    • 2 tablespoon Apple Cider Vinegar
    • 2 teaspoon Vanilla Extract

    Instructions

    chocolate chip cream cheese filling

    • Adjust the oven rack to the 2nd level position (just above center) and preheat the oven to 350°F. Line 2 standard cupcake tins with cupcake liners. This recipe makes approximately 30 cupcakes so you will need to use one of the cupcake tins a 2nd time.
    • Using a hand mixer or stand mixer fitted with a paddle attachment, beat the cream cheese on medium-high speed until smooth and creamy (2-3 minutes).
      8 oz Cream Cheese
    • Add in the granulated sugar and egg and continue to mix until completely blended. Scrape down the sides of the bowl as necessary.
      ½ cup Granulated Sugar, 1 Large Egg
    • Fold in the chocolate chips with a spatula. Set to the side.
      6 oz Semi-Sweet Chocolate Chips

    chocolate cupcakes

    • Using a hand mixer or stand mixer fitted with a paddle attachment mix together the all-purpose flour, unsweetened cocoa powder, baking soda, and granulated sugar on low-medium speed .
      3 cups All-purpose Flour, ½ cup Unsweetened Cocoa Powder, 2 teaspoon Baking Soda, 2 cups Granulated Sugar
    • On low speed, add in the eggs, vegetable oil, water, apple cider vinegar, and vanilla extract. Mix until just combined. The batter will be on the thin, runnier side.
      2 Large Eggs, ⅔ cup Vegetable Oil, 2 cups Water, 2 tablespoon Apple Cider Vinegar, 2 teaspoon Vanilla Extract
    • Using a cookie scoop, fill the cupcake liners no more than ½ full, then top with 1-2 tablespoons of the cream cheese filling.
    • Bake for 22-24 minutes at 350ºF.
    • Remove from the oven and cool for 10 minutes in cupcake tin. Then transfer to wire rack and allow to cool completely.
    • This makes roughly 30 cupcakes, so you will need to repeat this process one more time. Alternatively, you can half this recipe to get roughly 15 cupcakes.

    Video

    Recipe Notes

    Your eggs should be at room temperature before starting
    The cream cheese should be softened and at room temperature. If it's still even the slightest bit cold, it will leave small lumps in the filling and look like cottage cheese.
    Fill the cupcake liners only half way full to leave room for the dollop of cream cheese filling.
    This simple and delicious black bottom cupcakes recipe can easily be made in a 13" x 9" x 1" baking pan. Bake at 350°F for 45 minutes.
    Recipe adapted from the 1992 St. Andrew's Heavenly Delights Cookbook.
    DID YOU MAKE THIS RECIPE?Mention @beyond.the.butter and tag #beyondthebutter!
    Overhead closeup image of black bottom cupcakes randomly placed on gray background | All Images © Beyond the Butter™

    More cupcakes & muffins

    • Devil's Food Cupcakes with Peanut Butter Frosting
    • Bakery Style Chocolate Chip Muffins
    • Bakery Style Lemon Blueberry Streusel Muffins
    • Super Moist Carrot Cake Cupcakes

    © All images & content on BeyondtheButter.com are copyright protected. You may not republish, redistribute, or otherwise use any images, recipes, or content, in part or in whole, without express written permission from the author. Beyond the Butter® is a registered trademark of Jennifer Switzer. All rights reserved. For more information, please read my Policies page.

    Reader Interactions

    Comments

    1. Elsa says

      August 17, 2018 at 9:31 am

      5 stars
      I loved this recipe! It was easy to put together, and tasted fantastic. The cupcake part was moist, and the cheesecake filling on top creates a beautiful effect, so there’s no need for frosting (I love that part—more cake! + bake and go). I’ve switched the measurements to grams (only bake by weight), and put this recipe in my folder of ‘keepers’. Thanks for sharing, Jen!

      Reply
      • Jennifer says

        August 17, 2018 at 11:21 pm

        You're very welcome, Elsa! I'm so glad you loved it! Have a great weekend!

        Reply
      • Shelly says

        June 14, 2022 at 10:21 pm

        Been making these for years, family and friends love them! Your recipe is all the same except no eggs in the cake mix. I believe this what makes the cream cheese fall down in the middle. Not sure

        Reply
    2. Camila says

      March 08, 2019 at 9:24 pm

      5 stars
      These cupcakes look so beautiful!

      Reply
      • Jennifer says

        March 09, 2019 at 1:46 pm

        Thanks Camila! These are my all time favorite cupcakes ever! And no frosting needed either!

        Reply
    3. Naythar says

      June 12, 2019 at 2:24 am

      Any substitute for the apple cider vinegar?

      Reply
      • Jennifer says

        June 12, 2019 at 8:02 am

        I have not tried this, but I've read you can substitute apple cider vinegar with lemon juice. It's not a 1:1 ratio though. For the 2 tbsp of apple cider vinegar this recipe calls for, you could use 1 tbsp. of lemon juice or white vinegar.

        Reply
    4. Rose says

      August 23, 2019 at 11:01 pm

      5 stars
      I've made this recipe twice now and we love them! So easy and so yummy. Fun to make with my preschooler. I added a pinch of salt to the batter the second time and they tasted even better. Really light and moist.

      Reply
      • Jennifer says

        August 26, 2019 at 9:05 am

        This makes me so happy Rose, thank you! I love that you make them with your preschooler too! So much fun!

        Reply
        • Tansy says

          September 22, 2020 at 11:13 pm

          I just made these, they were great but my cream cheese mix was a bit watery and 2 I did not see my chips at all. Like they melted. Would love to try they again.

    5. Lauren Masters says

      November 17, 2019 at 6:06 pm

      5 stars
      Wonderful wonderful dessert, perfect for sharing, no mess! 5 stars!! Best served chilled - brings the cheesecake and chocolate chips to attention.

      Reply
      • Jennifer says

        November 19, 2019 at 11:20 am

        I'm so happy you loved them! They've been a favorite since I was a kid! Next time I make them I'll have to try them chilled - great idea!

        Reply
    6. Fira says

      November 24, 2019 at 2:59 am

      Hello. I'm so excited to try this recipe, thabk you very much for sharing. However, I'm scared thay my oven is not big enough to back all the cupcake all together, it jusg can only fit 12 cupcake tin. So, can I leave the battee outside first while waiting the one in oven baked completely?

      Reply
      • Jennifer says

        November 24, 2019 at 9:20 am

        Hi, thanks for your question! I haven’t had to do this, but I don’t think it would hurt. I wouldn’t wait much past the 22-24 minutes to bake them though. An alternative would be to half the recipe, and make them twice. I hope you love them as much as I do!❤️

        Reply
    7. Rachael says

      April 04, 2020 at 9:25 pm

      5 stars
      I loved these cupcakes and we’ll be sure to make them again! The chocolate chips and the cheesecake make the cupcake gooey and all sorts of delicious in the center! They also paired very nice with some vanilla bean ice cream:) this recipe was very easy to follow and simple to make - perfect!!!

      Reply
      • Jennifer says

        April 05, 2020 at 8:50 am

        Thank you so much, Rachael! I'll have to pair them with some vanilla bean ice cream next time! That sounds good!

        Reply
      • Nicole says

        April 06, 2020 at 9:37 pm

        Looks delicious! Quick question, how do you store leftovers?

        Reply
        • Jennifer says

          April 07, 2020 at 7:03 am

          Thanks! Keep them stored in an airtight container either at room temperature or the refrigerator for 2-3 days.

    8. Amy says

      April 05, 2020 at 12:11 pm

      5 stars
      I have tried multiple recipes on the internet for Black Bottom Cupcakes and these are, by far, the best I have tried! The chocolate cupcake crumb was moist and there were no issues with the cream cheese filling (as I have had with prior recipes). I have not been able to find a recipe that balanced both components. I have been an avid baker for over ten years - this is definitely a recipe you can trust! Since it’s a quarantine, to conserve baking supplies, I halved the recipe per recipe notes. I used parchment paper liners I purchased previously from Amazon. Look forward to trying more from Beyond the Butter.

      Reply
    9. Sammi says

      April 24, 2020 at 8:06 pm

      5 stars
      We absolutely love this recipe! Our friends that we shared them with enjoyed them too.

      Reply
    10. Mel Cee says

      April 26, 2020 at 9:29 am

      4 stars
      This recipe was super easy to follow and yielded almost 30 cupcakes! Next time, I'll cut in half. The hardest part was filling the cupcake tin but I appreciated the tip to fill in half way. I used a small ice cream scooper for the cream cheese. I refrigerated them overnight and I feel like they tasted better the next day!

      Reply
    11. Carol T says

      June 12, 2020 at 1:31 pm

      5 stars
      Perfect recipe, exactly as is.

      Reply
      • Jennifer says

        June 15, 2020 at 3:14 pm

        Thank you for making them, Carol! They're my all time favorite cupcake!

        Reply
    12. Kat says

      August 29, 2020 at 5:37 pm

      5 stars
      These are seriously delicious! And so easy to make. Will definitely be making them again.

      Reply
      • Jennifer says

        August 31, 2020 at 2:57 pm

        Thank you so much, Kat!

        Reply
    13. Donna says

      September 16, 2020 at 5:08 pm

      Just saw this now and would love to try it. Was wondering if I can cut down the sugar in the cupcake batter to just 1 cup? Or if you have any alternatives for it? Thank you!

      Reply
      • Jennifer says

        September 17, 2020 at 10:48 am

        Hi Donna, no I'm sorry I don't have any alternatives. Because this makes close to 30 cupcakes, you could half the recipe, which would also then half the amount of sugar.

        Reply
    14. Tansy says

      September 22, 2020 at 11:15 pm

      4 stars
      I just made these, they were great but my cream cheese mix was a bit watery and 2 I did not see my chips at all. Like they melted. Would love to try they again.

      Reply
    15. Kim says

      January 30, 2021 at 1:35 pm

      Making these for a kids birthday. Can they be frosted??

      Reply
      • Jennifer says

        January 30, 2021 at 2:14 pm

        Hi! Yes, they can be, but I’ve never had them this way. The cream cheese filling basically gives them that sweet balance frosting will do with a regular chocolate cupcake. If you do frost them I wouldn’t go super heavy with the frosting or it might end up being overly sweet. Hope this helps!

        Reply
    16. Sarah says

      May 10, 2021 at 1:17 pm

      Hi, these look delicious! There's only 3 of us at home, so if the recipe is halved, should I still use a 13x9" pan for baking? Or would a 8" pan be better? Any idea on the baking time?
      Also, does this cake freeze well? Thank you!

      Reply
      • Jennifer says

        May 10, 2021 at 6:34 pm

        Hi! Thank you so much! I'm sorry I'm not sure what pan size would be best or baking time for halving this recipe as I didn't test it this way. I've never frozen the cupcakes before, but I imagine they would freeze well. I would suggest double wrapping them in plastic wrap them keep them stored in an airtight container.

        Reply
    17. Ann says

      May 11, 2021 at 4:18 pm

      Hi, just wondering if I can use spreadable cream cheese for this recipe? Thank you

      Reply
      • Jennifer says

        May 12, 2021 at 10:10 am

        Hi! No, I don't recommend using a spreadable (tub) cream cheese for this recipe. It tends to have higher water content and, with some, more salt. They're really just meant for adding to bagels, etc. For baking, it's always best to use a block.

        Reply
    18. Debbie says

      July 18, 2021 at 11:50 am

      If I bake in a 9x13 pan do I grease and flour it?

      Reply
      • Jennifer says

        July 19, 2021 at 10:05 am

        Yes, I definitely would!

        Reply
    19. Sharon says

      March 06, 2022 at 11:55 pm

      Very good and moist! Definitely make again. I cut out 1/2 cup of sugar this time and will add some salt next time. Great for breakfast too. Thanks for the recipe.

      Reply
    20. Linda says

      July 05, 2022 at 8:44 pm

      I used to make these as a special treat for the kids at Christmas every year but now they are all grown and have children and THEY dont do sweets, esp with white flour. Well, I am making a cake tonight and thought I could make the cream cheese filling and swirl it into the cake..... I will let all know how it turns out..

      Reply
    21. Nancy DeMent says

      July 13, 2022 at 12:27 pm

      I’ve been making these cupcakes for years and I always have some cheesecake filling left over. What can I do with it?

      Reply
      • Jennifer says

        July 13, 2022 at 7:06 pm

        You could do a number of things! You add it to my better-than-box mix brownies recipe (or one you prefer), add it to my single layer chocolate cake recipe, or use it for my small batch black bottom cupcakes recipe. Of course, you can always freeze it too (I'd say for up to a month), then bring it to room temp in the fridge until thawed before using. Hope these ideas help!

        Reply

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