Chocolate Salted Rye Thumbprint Cookies

Chocolate Rye Salted Thumbprints | A Sweet Spoonful

This past week I’ve been teaching a holiday gifts class at The Pantry, a cooking school here in Seattle. We’ve been spending each evening making butterscotch pudding, pâtes de fruit, fig and almond crackers and chocolate ginger cookies — and while I’ve loved getting back in front of students again, I think my favorite part has been the very beginning where we introduce ourselves and share one holiday treat we like to make or eat: the room buzzes with talk of spiced pfeffernüsse, buttery cashew toffee and boozy rum balls. Growing up, my mom made Baked Alaska for dessert every Christmas Eve and I grew so accustomed to it that I was surprised when I went away to college and learned that no one had really heard of it. In fact, when my new boyfriend (now husband) Sam joined us a handful of years ago, he seemed utterly baffled by the meringue-topped boob of an ice cream dessert that we’d pour cognac over and light on fire. But it was always my mom’s thing (and until tonight, when I asked her about why she began making it, I hadn’t realized that it was also my grandma Marge’s thing).

Zeke, my mom’s former handyman (he passed away a few years back), would always bring over a cookie plate filled with truly awful cookies, but he decorated them himself with colorful sprinkles and included a few dog bones, and the gesture felt quite grand for a man in his 80’s. Sam’s mom makes these fragrant buttery cookies called Nutmeg Logs that we’ve started to bake as well, and our friend Molly often brings by a tin she and her mom make each year that includes peppermint bark and a jammy sandwich cookie. Maybe your family’s thing was something you really loved, and maybe it wasn’t — it seems that part isn’t as important as the fact that it happened. And continued to happen. There’s such a comfort in that repetition, and today those things that help ground us feel more important than ever.

Dark Chocolate Salted Rye Thumbprints | A Sweet Spoonful

Oliver was just a little over a month old when last Christmas rolled around so I gave myself a big ol’ pass on pretty much everything, but this year I’m feeling a bit anxious about the fact that we don’t really have our thing. The weekend after Thanksgiving, Sam and I had a talk and he reminded me that traditions often come about by accident — they’re so often not the things you plan for, but the things that end up happening for one reason or another … and you end up keeping them around. Like how we always go to Ivar’s after we pick out our tree each year for fish and chips. Not because they’re particularly famous or something either of our families ever did – but more that one year we were particularly cold and hungry after getting the tree tied to the car and Ivar’s was right next door, beckoning us with the promise of hot chowder, halibut and those blessed, very hot “chips.”

Sam stood and rocked our two-week old Oliver for the duration of last year’s ritual Ivar’s visit, both of us holding our breath, ready to take our food to-go and bolt at any moment should he freak (he didn’t, and we felt on top of the world that we survived our first restaurant meal with him). This year, Oliver sat proudly in a high chair in the sweater I bought him for his first birthday, eating French fries and tartar sauce like it was his job.

Chocolate Salted Rye Thumbprint Cookies | A Sweet SpoonfulSo while I still don’t know how to cook a turkey, don’t necessarily have a cookie I’m particularly famous for, or any idea what to make for Christmas Eve dinner, I’m trying to encourage myself just to settle into it all. To let it happen to us, and trust that a few cookies, treats, and traditions will rise to the surface in their own time. Like the fish and chips. Or maybe even these reimagined thumbprint cookies we’ve been pretty fond of.

Chocolate Salted Rye Thumbprint Cookies | A Sweet Spoonful

In many ways I’m a bit of a thumbprint purist, often overriding my preference for baking with whole grain flours (except when it comes to these buckwheat beauties) for the Ina recipe, super buttery cookies rolled in sweet coconut and finished with a generous dollop of sweet jam. And while I love Ina’s cookies, I’ve been tinkering with a thumbprint made with chocolate and rye flour, filled with a dark chocolate ganache. Oh, and a sprinkle of flaky salt at the very end.

Chocolate Salted Rye Thumbprint Cookies | A Sweet Spoonful

The earthy flavor of Bob’s Red Mill dark rye flour pairs so well with chocolate (I also love it with apple and pear desserts), making for one soft, slightly crumbly cookie with that addictive chocolate/salt thing going on that I can’t seem to quit. Really, that’s the only nudge I need to bake another batch. And eventually another. I guess that’s how these traditions take hold, yes?

Chocolate Salted Rye Thumbprint Cookies | A Sweet Spoonful

A few brief notes: if you don’t have rye flour, these are really forgiving cookies so you can make them with whole wheat flour, spelt flour, kamut or buckwheat flour. I haven’t tried them with many gluten-free flours and that’s not necessarily my area of expertise, but I’d love to hear about any experiments or blends you end up making.

Chocolate Salted Rye Thumbprint Cookies

Chocolate Salted Rye Thumbprint Cookies

  • Yield: 22-24 cookies
  • Prep time: 25 mins
  • Cook time: 18 mins
  • Inactive time: 1 hr 25 mins
  • Total time: 2 hrs 8 mins

These holiday cookies are less sweet that a traditional thumbprint cookie, relying on a dark chocolate ganache filling instead of the more traditional sweet jellies or jam. They’re soft and slightly crumbly in texture, which I love in a good snacking or tea cookie. Turbinado sugar is chunkier than granulated sugar and won’t melt down in the same way — so it helps make the edges of these cookies look slightly sparkly – most appropriate for the season. If you have sanding sugar at home, that would work great to roll the cookies in as well (just don’t use it in the actual dough).


For the Cookies:

3 ounces chopped bittersweet chocolate (60-72%)
1 cup (135g) Bob’s Red Mill dark rye flour (or spelt / whole wheat flour would work, too)
1/2 cup (60g) All-purpose flour
1/2 cup (50g) dark unsweetened cocoa powder
1/2 teaspoon kosher salt
12 tablespoons (1 1/2 sticks) unsalted butter, at room temperature
1/2 cup (110g) turbinado sugar, plus more for rolling
1 large egg yolk
1 teaspoon pure vanilla extract
flaky salt (like Maldon), to finish

For the Chocolate Ganache:

3 tablespoons heavy cream
4 ounces chopped bittersweet chocolate (60-72% )
1/2 teaspoon pure vanilla extract


In a small heavy-bottomed pot over low heat (or in a microwave-safe bowl in the microwave), melt the dark chocolate, stirring often to avoid burning. Whisk until smooth and set aside.

In a small mixing bowl, whisk together both flours, cocoa powder and salt.

In the bowl of a stand mixer fitted with the paddle attachment, cream the butter and sugar on medium speed until pale and fluffy, about 3 minutes. Add the egg yolk and vanilla and beat a few times to combine. Scrape in the melted chocolate and beat until just incorporated. Slowly beat in the flour mixture until just combined. Cover bowl with plastic wrap and refrigerate until firm, about 30 minutes.

Preheat the oven to 350 F. Line a large baking sheet with parchment paper. Get a little bowl ready with extra turbinado sugar to roll the cookies in. Form balls using 1 tablespoon of dough for each, and roll in sugar. Place balls 1 inch apart on prepared baking sheet.

Use your thumb to press gently into the center of each cookie to create an indentation – be careful not to press all the way through the cookie and be sure the indentation is wide enough to hold the filling. The cookies may crack a little on the sides and that’s ok – that gives them character. If they crack significantly, I do a little quick push / pat back together.

Bake for 10 minutes, remove from oven and use your finger or the tip of a wooden spoon to reinforce the indentation if it’s started to puff back up in the baking process. Then place back in oven and bake until cookies are just set, about 8-9 minutes (they will still feel soft; they’ll firm up as they cool). Allow cookies to cool on baking sheets for 5 minutes. Transfer to wire racks to cool completely.

Meanwhile, make the chocolate ganache: In a heatproof bowl set over a pan of barely simmering water, melt the chocolate with the cream, stirring until smooth. Stir in the vanilla extract. Let cool until the mixture is thick and spoonable, like pudding, about 15 minutes. Gently spoon chocolate filling into the center of each cookie. Let stand until set, about 55 minutes. Sprinkle a pinch of flaky salt across the tops of each cookie. Cookies can be stored in an airtight container for up to 5 days.


  1. solveig

    Sounds delicious!
    Do you think you can replace the cream in the Chocolate Ganache with a non dary product, like oat milk or something like that?
    Thanks :-)

    1. megang

      You know, I haven't tried it but I think it will work! It's largely chocolate that's melted and then left to cool and firm back up, so I have a hunch it's going to work. Let me know how they turn out! Enjoy.

  2. Lori

    I can't wait to make these! And dust off my grandmothers's recipe for Ranger cookies, which she made every year for my Uncle Larry. Happy holidays to you and your family. xo

    1. megang

      Thanks so much, Lori! Happy holidays to you, too! xo

  3. mcs3000

    Love the pic of Sam + little O - beautiful!

  4. Rebeca

    As far as I'm concerned, rye flour and chocolate are a match made in heaven, so I'll have to give them a try! Do you think I could substitute the butter? I'd like to make them for someone with a milk allergy.

    1. megang

      Hi, Rebecca. Agree re: rye + chocolate: an easy marriage. So I haven't tried these with a non-butter alternative but I have a feeling they'd work. Are you thinking something like coconut oil? Here, we're not so much creaming the butter and sugar to get lift -- we're sort of just mixing them until combined well so I have a feeling coconut oil might work. I'd love it if you report back on what you found ... again, just going with an educated guess here as I haven't tried it. Happy holidays + I hope you enjoy the recipe.

  5. Lola

    In France, baked Alaska is called omelette norvégienne. I remember that it was considered a dessert for big occasions during my childhood (in the 80's). I haven't seen it anywhere in France recently.
    In my family, Saint-Honoré is the traditional dessert for Christmas - bought at the local pâtisserie, not home made. Family members fight over how many choux and and how much chantilly one can get, it is always a fun way to end the evening...
    Happy holidays to you and your family!

    1. megang

      Oh I've had Saint-Honore and love it - so simple and delicious. My Dad likes Bouche de Noel, so we often have that when we spend the holiday at his house. Happy holidays to you, too, Lola!

  6. Amy

    Ok, I've read this recipe a handful of times, and I've actually got rye flour in my pantry, and I keep coming back to it as a possibility to add to my Christmas cookie tins, but I think the ganache step is what's holding me back. Plus I'm trying to avoid dairy where I can, and this takes it up a level. Do you think I could just use a raspberry jam for the centers?

    1. megang

      YES, Amy! I think they'd be delicious. Do it!

      1. Amy

        These are SO good. (And forgiving. The butter was way too soft when I started to make them, but they turned out anyway!) I'm making another batch tonight. The raspberry jam- I splurged for organic spreadable fruit- was a perfect match.

        1. Amy Sigmon

          Just looked up this recipe to do some last minute baking this weekend. I remembered I put jam in the middle, but couldn't remember how I came to that decision. Scroll down to the comments section...sure enough, here's that exchange! Thank goodness for blogs.

  7. Becki

    I made these tonight and I love them! They are so tasty and the texture (a little crumbly but not too delicate) is just right. I am a big fan of ganache on anything and salt on chocolate, but for these cookies it's almost not needed. They're that good!

    I used 2T of plain rice milk instead of cream in the ganache and it set up just fine. And thank you for including weights for the ingredients - I'd much rather use the scale than dirty up measuring cups!

  8. Kristie

    I'm planning to make these cookies tomorrow using buckwheat flour in place of rye. Buckwheat and rye weight different amounts, so should I measure the buckwheat by weight or volume. I tried to search this on Google, but couldn't find any answers. Also, I'm curious how you measure your flour. Yous say 1 cup of rye flour is 135g, but two other sources I've checked say it's around 105g (do you pack it in?). A cup of buckwheat is 120g, so it's in the middle - Help!

    1. megang

      Hi, Kristie! Great questions. So in regards to the flour coming in at different weights, this really depends on the brand of flour, crop, age etc. So it's normal to have a little variance there. As for what to do in regards to weight / using buckwheat tomorrow, use the same weight that the original recipe says (so you'll measure out 135g buckwheat). The dough is going to be a little crumbly and that's ok. Let me know how they turn out! Happy holidays.

      1. Kristie

        Thanks, Megan! I made them with buckwheat and gluten free measure-for-measure flour and they turned out great! Sadly, my husband can no longer eat gluten, and he's very excited to have these cookies at Christmas, as he won't be able to eat most of the other sweets that people bring. Happy holidays to you and your family!

        1. megang

          Hi, Kristie! So glad the cookies worked out for you all and your husband enjoyed them. Makes my day! Have a wonderful holiday!

  9. Kasey

    Lovely sentiment! I love traditions but I have to admit that the best ones were never really intended to be. I'm not sure we have our 'thing' this year, but I'm ok with that :) Happy holidays to you and yours! xo

  10. Jessica

    Just an fyi, ganache can be made with any liquid - it doesn't have to be dairy. You could use fruit juice or tea or a non-dairy milk. The key is to have the liquid and chocolate be equal in temperature before stirring. So you can heat your liquid, pour it over your chocolate and let it stand for a few minutes before whisking together. A 1:1 ratio of chocolate to liquid will give you a nice spoonable consistency; 2:1 will be pipable for writing on cakes; 1:2 will be thinner for glazing a cake.

    1. megang

      Fantastic. Thanks so much for the great info., Jessica!

  11. Ali

    My daughter has celiac, so I replaced the rye with buckwheat and the all purpose with millet and tapioca starch. I love the blend of buckwheat and chocolate even more than rye. Definitely a good alternative for something different and easily made gluten-free if required.

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