Mini Cheesecake Cookie Cups

Mini Cheesecake Cookie Cups

A soft graham cracker crust with the simplest cheesecake filling makes these cheesecake cookie cups the perfect cookie plate surprise.

A soft graham cracker crust with the simplest cheesecake filling makes these cheesecake cookie cups the perfect cookie plate surprise.

Especially during the holiday season, I crave everything with cinnamon and other warm spices. Bonus points for cookies with molasses in them, like graham crackers and our super soft chocolate ginger molasses cookies.

Nothing goes with those spices better than cheesecake, but I’ve got cookie gift boxes to fill and cheesecake just doesn’t travel. I remember years ago making soft graham cracker cookies to make copycat moon pies, and they were a huge hit. One local parent actually asks me about them nearly every time I see him. For real.

A soft graham cracker crust with the simplest cheesecake filling makes these cheesecake cookie cups the perfect cookie plate surprise.

Why bake them in a muffin tin?

I started out making almost these exact cookies but as thumbprints. You can actually bake the cheesecake filling right in the middle of the thumbprints, and it does work.

But you just can’t get enough cheesecake filling in there to satisfy. Instead of thumbprints, though, I was sure I could bake these cheesecake cookie cups with a deeper well, and bake a true cheesecake filling together with the cookie dough.

A soft graham cracker crust with the simplest cheesecake filling makes these cheesecake cookie cups the perfect cookie plate surprise.

I learned long ago how to make a cookie recipe into cookie cups. I baked them empty and fill them with no-bake cheesecake or whipped cream and berries soon before serving. They make such an impressive presentation but are super easy once you get the technique.

The beauty of baking these in a muffin tin is that the cheesecake filling and the cookie dough rise together in the oven. I use very little leavening in the cookie dough and only an egg yolk in the filling instead of a whole egg. That helps the cookies keep their shape and form. And the filling is deep enough to actually taste like cheesecake.

You don’t want someone to bite into one of these cookie cups and say, “Tastes great. What did you say was in the center?”

A soft graham cracker crust with the simplest cheesecake filling makes these cheesecake cookie cups the perfect cookie plate surprise.

What is the dough like to work with?

This cookie dough is not dry, but it’s not wet, either. The ingredients are balanced just right, which makes it especially important that you bake by weight, not volume (and use one of my recommended all purpose gluten free flour blends). 

When you mix the dough, it will stay in wet crumbs until you knead it together with your hands. In that way it’s similar to our strawberry white chocolate chip cookies. Trust the process, though. There are no mistakes in the recipe. 

A soft graham cracker crust with the simplest cheesecake filling makes these cheesecake cookie cups the perfect cookie plate surprise.

A word about mini muffin tins

We talked about miniature muffin tins when we made our two bite gluten free brownies, but it bears repeating here. They are not all created equal. 

You can use any miniature muffin tin to make these cheesecake cookie cups. You can even shape them similarly to how you would using the muffin tin, and bake them (filled) on a baking sheet (they will flatten a bit, though).

A soft graham cracker crust with the simplest cheesecake filling makes these cheesecake cookie cups the perfect cookie plate surprise.

But you’ll have the best luck with these if you can make them in a miniature muffin tin with relatively deep wells and gently sloped walls (not entirely vertical). I usually use a USA Pans brand miniature muffin tin, but I just bought some “Good Cooks” brand that I’m kind of hopeful about (You know the brand you often find in grocery stores? I really like it!).

My current favorite standard muffin tin is a nonstick pan made by Wilton that isn’t too dark and isn’t too light. I’m tempted to try their miniature muffin tin, but it’s not like anyone is begging me for mini muffin tin recommendations so it’s hard to justify yet another tin!

A soft graham cracker crust with the simplest cheesecake filling makes these cheesecake cookie cups the perfect cookie plate surprise.

Ingredients and substitutions

I’ve got good news and bad news about substitutions, but mostly bad news. 😔Let’s jump right in.

Dairy-free: First, the good news is that you can make the cookie cup portion of this recipe dairy-free by replacing the unsalted butter with half (56 g) Earth Balance Buttery Sticks and half (56 g) nonhydrogenated vegetable shortening. You could probably also try using all Melt brand vegan butter. It’s worth experimenting.

The cheesecake filling is an entirely different story. Cheesecake is the third rail of dairy-free baking. I’ve tried soooooo many recipes and variations of recipes, and absolutely nothing has tasted like actual cheesecake to me.

Absolutely none of the dairy-free cream cheeses taste authentic to me. I’ve tried them all. I’ve also tried cashew-based dairy-free cheesecake fillings. Some taste pretty good, but they’re just not cheesecake to me. I’m so sorry to disappoint!

Egg-free: This is a hurdle, too. Both the cookie cups and the cheesecake filling call for egg yolks. Egg whites can often be replaced by aquafaba, and whole eggs with a “chia egg.” But egg yolks are hard. I’ve never had much luck. If you have a favorite egg-free egg yolk substitute, please let us know in the comments!


A soft graham cracker crust with the simplest cheesecake filling makes these cheesecake cookie cups the perfect cookie plate surprise. #glutenfree #cookies #Christmas #cheesecake

Like this recipe?

Prep time: Cook time: Yield: About 30 cookies


For the cheesecake filling
4 ounces cream cheese, at room temperature

6 tablespoons (75 g) granulated sugar

1/8 teaspoon kosher salt

1 egg yolk (25 g) at room temperature

For the cookie cups
2 2/3 cups (375 g) all purpose gluten free flour (I used Better Batter)

1 1/2 teaspoons xanthan gum (omit if your blend already contains it)

1/2 teaspoon baking powder

1/4 teaspoon kosher salt

1/3 cup (67 g) granulated sugar

2/3 cup (145 g) packed light brown sugar

8 tablespoons (112 g) unsalted butter, at room temperature

3 tablespoons (63 g) honey

2 tablespoons (42 g) unsulphured molasses

1/2 teaspoon pure vanilla extract

2 eggs yolks (50 g, weighed out of shell) at room temperature

Lukewarm water by the half-teaspoonful, as necessary

Melted chocolate, for drizzling (optional)


  • Preheat your oven to 350°F. Grease the wells of a 24-well miniature muffin tin and set it aside.

  • First, make the filling. In a medium-size bowl, place the cream cheese, sugar, and salt, and beat with a handheld mixer (or a whisk, vigorously) until light and fluffy. Add the egg yolk and whisk by hand until just combined. Cover the filling and set it aside.

  • To make the cookie dough, in a large bowl, place the flour, xanthan gum, baking powder, salt, and granulated sugar, and whisk to combine well. Add the brown sugar and mix, breaking up any lumps. Create a well in the center of the dry ingredients, and add the butter, honey, molasses, vanilla, and egg yolks, and mix to combine. The dough should come together and be thick but soft. If necessary to bring the cookie dough together cohesively, knead in some lukewarm water by the half teaspoonful.

  • Scoop the dough into portions about 2 teaspoonfuls each, roll each mound of dough into a ball between your palms, and place in the center of each of the prepared wells of the miniature muffin tin. With a clean index finger, press a hole into the center of each ball of dough. Using your index finger and thumb, pinch the dough to thin the sides and press them toward the edges and bottom of the muffin well. Using a small spring-loaded ice cream scoop or two spoons, fill each of the wells about 3/4 of the way full with the cheesecake filling. Repeat with the remaining balls of dough and cheesecake filling. You will need to repeat the process with about 6 more wells of the muffin tin in a second round.

  • Place the muffin tin in the center of the preheated oven and bake until the cookie cups are just beginning to brown around the edges and the filling is mostly set (about 12 minutes). Do not overbake. Remove from the oven and allow to cool on the baking sheet for at least 10 minutes or until firm. To remove the cookie cups from the muffin tin, twist them in the wells to loosen them, then pry them out with a toothpick inserted gently on the side of the cookie cups. Chill the cookie cups until the filling is firm, about 1 hour. Drizzle lightly with melted chocolate, if desired.

  • These cookies can be frozen in a single layer on a rimmed baking sheet, then piled into a freezer-safe zip-top bag for longer storage. They don’t actually freeze completely solid, so in a pinch, they can be eaten right out of the freezer. What? Don’t judge.


Comments are closed.

  • Suzey
    December 9, 2018 at 6:16 AM

    These are great, I may try them with canoli pie filling, what do you think? Do you think they would still freeze? And some salted caramel ones maybe.

    • Nicole Hunn
      December 9, 2018 at 3:11 PM

      That should work, Suzey (assuming you’re talking about my cannoli pie filling, which is similar in texture to cheesecake). Great idea!

  • Kathy
    December 3, 2018 at 8:26 AM

    Have you tried Trader Joe’s Plain Classic Vegan Cream Cheese Alternative?
    It works great in GF Mac and cheese, but haven’t tried to make cheese cake with it yet.

    • Nicole Hunn
      December 3, 2018 at 11:42 AM

      Hi, Kathy, no I haven’t! I have to be honest: I didn’t even know that they sold that. I’ll have to check it out. If you like it in mac and cheese, it’s definitely worth trying in cheesecake.

  • Paige
    December 3, 2018 at 1:40 AM

    Really excited about trying this recipe, just wondering what I can substitute for the unsulphered molasses, maple syrup, maybe?

    • Nicole Hunn
      December 3, 2018 at 8:03 AM

      The molasses is a very large part of what gives the cups their graham cracker-like flavor, Paige. I’ve never tried substituting it, but you could try honey. Maple syrup is a much different consistency so it’s not a proper substitute.

  • Rebekah
    December 2, 2018 at 7:24 PM

    I plan to try these using a basic inexpensive dairy-free cream cheese like Tofutti. 5 of us MUST eat dairy-free, plus I need the GF crust. I love every recipe I have tried from your long list of goodies. Thanks for inspring us to bake GF and providing delicious variety to live GF easily!

    • Nicole Hunn
      December 3, 2018 at 8:04 AM

      Thank you so much for the kind note, Rebekah. I’d love to hear how you make out with the Tofutti cream cheese sub. Hopefully well!

  • Carin
    December 2, 2018 at 11:26 AM

    Hi, Nicole. These look fabulous! My question is if they need refrigeration or can they be stored at room temperature. Thank you for all of your inspiring recipes!

    • Nicole Hunn
      December 2, 2018 at 11:43 AM

      Hi, Carin, like any cheesecake, I think the filling tastes best when kept chilled. But nothing terrible will happen to them at room temperature, and they can certainly be packed into cookie boxes or served on a cookie plate. Hope that helps!

  • Meredith
    December 2, 2018 at 10:52 AM

    (Also the Wilton mini-muffin is my favorite – great results like their larger ones!)

    • Nicole Hunn
      December 2, 2018 at 11:20 AM

      So good to know, Meredith! I’m very tempted to buy them, but I think I’ll see first how I like my Good Cooks brand mini muffin tins. They’re so inexpensive and usually work great.

  • Meredith
    December 2, 2018 at 10:50 AM

    Although not totally dairy free, some people tolerate goat milk when they can’t tolerate cow milk. I have been struggling with the cream cheese dilemma baking for my sweetie for years. I finally tried mixing chevre with some coconut cream to make a french toast casserole and it tasted perfect. I’ll give it a go with these and report back, if you’re interested!

    • Nicole Hunn
      December 2, 2018 at 11:19 AM

      If you can have goat milk, Meredith, Trader Joe’s makes a goat cheese spread that is completely delicious and really does taste a lot like cow’s milk cream cheese. I’d try that!

  • Laurie in PA
    December 2, 2018 at 10:25 AM

    I definitely want to make these, but I’m curious about why the intro says graham cracker crust (I bought some GF graham style crackers for that purpose and am looking for good recipes) since the crust recipe uses regular flour. Also, is it ok to sub neufachatel cheese to lower the fat content in the filling?

    • Nicole Hunn
      December 2, 2018 at 11:17 AM

      Hi, Laurie, this is a homemade soft graham-style cookie crust, made from scratch. True “graham flour” would never be gluten free. I’m not entirely sure about the lower fat cream cheese style spread, to be honest. The whole thing only has 4 ounces of cream cheese, so if you can, I’d go for the real thing.

  • Vicki
    December 2, 2018 at 8:25 AM

    Nicole, please disregard the first comment I left about the xanthan gum. For some reason it doesn’t show up in the recipe here, but it did show up on the printed recipe (about leaving out the xanthan gum if your blend already has it).

    • Nicole Hunn
      December 2, 2018 at 11:18 AM

      Hi, Vickie, I think it’s because the recipe you’re looking at on the screen is your computer’s cached version, and a bit earlier this morning I edited the recipe with the note about xanthan gum. So sorry for the confusion!

  • Vicki
    December 2, 2018 at 8:19 AM

    Nicole, do we add the 1 1/2 teaspoons of xanthan gum if our flour blend already has it?

  • Beverley Baines
    December 1, 2018 at 11:21 PM

    As I don’t have a mini muffin tin, just a regular one, how much longer would I have to bake them?

    • Nicole Hunn
      December 2, 2018 at 7:42 AM

      Hi, Beverly, Oddly I haven’t ever tried these in a full-sized standard 12-cup muffin tin, but based upon my experience with these sugar cookie cups, I’d suggest checking at 15 minutes.

  • Carole
    December 1, 2018 at 9:46 AM

    Hi Nicole,
    Could agave be used in place of the honey in this recipe?

    • Nicole Hunn
      December 2, 2018 at 7:38 AM

      Probably, Carole? I haven’t tried that but it’s worth a shot!

  • Jean Fater
    December 1, 2018 at 8:04 AM

    Hi Nicole, These sound fabulous! Do we still need the xanthan gum if we are using the Better Batter? Usually there is a note about omitting it but not here. I just want to be sure. Thanks so much for all you do!

    • Nicole Hunn
      December 2, 2018 at 7:34 AM

      Oooh good point, Jean. No no if you use a blend that already contains xanthan gum, omit it from the ingredient list. I will edit the recipe. Thank you so much for pointing that out!

  • Ana
    December 1, 2018 at 6:23 AM

    I completely agree! Cheese (in any form) is the one thing that just can’t be substituted. I’m gluten/dairy-free, but I make the dairy exception during the holidays. I refuse to go without homemade mac & cheese or delicious cheesecake!

    • Nicole Hunn
      December 2, 2018 at 7:37 AM

      I actually think it’s possible to make a really good vegan mac and cheese (it’s not exaaaaactly the same but it can be really really good). But really good dairy-free cheesecake eludes me. I did buy a Daiya brand frozen dairy-free cheesecake a while back, but I’m afraid to try it because it was super $$ and what if it’s terrible? 🙃

  • Marynia Goertz
    November 30, 2018 at 4:32 PM

    I was searching for a cookie crust to make leftover pecan pie filling into mini pies and of course you delivered today! Would the crust be ok if I baked longer to accommodate the pecan pie filling? I’d probably make regular muffin-cup-size pies.

    • Nicole Hunn
      December 2, 2018 at 7:36 AM

      That’s a super interesting idea, Marynia. I think it would be fine, and actually think the filling would back at about the same rate as the cheesecake filling since such a small amount compared to a whole pie. If you’re at all concerned, lower the oven temperature a bit, and just make sure that none of the crust peeks out above the top of the muffin tin well.

  • Tia
    November 30, 2018 at 1:39 PM

    Hi Nicole,
    Have you ever tried Kite Hill cream cheese? It’s not exact but it’s the closest I’ve found to the real thing. I love it! I plan to try it in this recipe. I’ll let you know how it is!
    Thanks for all the great recipes!


    • Nicole Hunn
      November 30, 2018 at 2:02 PM

      I have, Tia! I’ve also tried their yogurts, and I’m afraid I didn’t care for any of them. One I haven’t tried that might be promising (since I’ve made and tried many of her other products) is Miyoko’s Kitchen brand. I also absolutely love Violife vegan cheeses, and I see that they also make a cream cheese-type product. I’d love to try that one, too.

Where should I send your free guide?

By entering your email, you're agreeing to our Privacy Policy. We respect your email privacy, and will never share your information.