Fudgy Chocolate Thumbprint Cookies

These classic Fudgy Chocolate Thumbprint Cookies will quickly become one of your favorites. Flecked with chopped chocolate, the shortbread-like cookie base holds a rich fudgy center.

I’ve never seen another chocolate thumbprint cookie like this one. It’s been in my family for decades. (Thanks, Mom! xoxo) Near as we can tell, it came from Mom’s 1963 Good Housekeeping Cookbook, but she copied the recipe to a card in her recipe box.

There is no leavening agent (like baking soda) or eggs in this recipe. This yields a finely textured cookie that is in perfect harmony with the fudgy filling.

Fudgy Thumbprint Cookie Basics

This recipe is two steps:

1. Mixing and baking the cookie base
2. Melting the fudgy center and filling the cookies

Making the cookie base

I like to prep all of my ingredients first. It helps to speed up the process as well as keeping me organized. (You know, did I put the vanilla in already???)

A word about the fat used in this recipe

This recipe calls for margarine. Please don’t substitute it because it’s highly likely to not turn out properly. This is the only thing I ever cook with margarine – I’m a diehard butter lover. But trust me, it doesn’t work otherwise.

You need actual margarine, and a high quality one, at that … and NOT one of the spreadable or light varieties! I often use Land O’ Lakes. DO NOT use a product like Country Crock or I Can’t Believe It’s Not Butter – the water content is far too high!

Prep your ingredients. Stir together the flour and salt. Chop the chocolate chips for the cookie base (not the filling) into small pieces. You can do this by hand or with a mini chopper. Just be sure to not chop it to dust. Conversely, pieces that are too large might crack your dough.

In a mixer bowl, cream the margarine and brown sugar with the vanilla until light and fluffy. Creaming is a baking term that means to beat together until emulsified and light in texture. For more on creaming, check out a further explanation of it in my recipe for Chewy Chocolate Chip Cookies.

Alternately mix in the flour and milk. Stir in the chopped chocolate last. Don’t overmix! You don’t want a tough cookie.

This dough enjoys being chilled, so pop it in the fridge for an hour or two. You can easily refrigerate it overnight, too! Let it sit out on the counter for about 30 minutes so it’s not hard to work with. No time to chill? No worries, just roll them quickly.

Bake at 350 degrees for 10-12 minutes until the bottoms of the cookies are barely golden. If the depression in the cookies baked out too much, you can give them a quick tap with the wine cork immediately upon removal from the oven.

Cool on the sheet pan for a few minutes. If you like, simply pick up the whole sheet of parchment including the cookies and place it on a cooling rack. That will make cleanup easier after filling the cookies.

What’s this about parchment paper, anyway?

I always bake my cookies on precut parchment paper. They bake much more evenly and cleanup is a breeze. I only purchase it in the precut half sheet pan size (which is what a standard home baking sheet pan is. A full sheet pan is what professional kitchens use and it’s huge.) Don’t even bother with the parchment on a roll. You’ll spend half your time just getting it to somewhat fit. Plus, it’s more expensive per foot.

Make the Fudgy Chocolate Thumbprint Filling

If you’ve never used a double boiler, it’s nothing more than a heatproof bowl or pot fitted over another pot. There is about 1″ of nearly simmering water in the bottom pot. It’s designed to gently cook something without direct heat from a burner.

There should be no gaps between the top bowl and the bottom pot, or otherwise the valuable steam that is your heating agent will be lost.

Place all of your filling ingredients (chocolate chips, shortening, corn syrup, water and vanilla) into the bowl of the double boiler and heat the water in the pot. As it melts, stir it smooth.

You can also do this in the microwave, but you must be very careful. It can quickly burn in spots and the chocolate might seize (a culinary term meaning to clump and break its emulsion.)

Filling the cookies

Push your cooled cookies together so they’re touching on the parchment. Set your whole double boiler on a hot pad beside the cookies – leaving the bowl of filling sitting over the steaming water in the boiler will continue to keep the filling warm.

Using a soup spoon or another deep spoon that’s not too large, fill the cookies. I can usually fill 3 cookies from one dip of a soup spoon. You’ll quickly get the hang of it.

Allow the cookies to sit untouched for at least an hour.

Can Fudgy Chocolate Thumbprint Cookies be frozen?

Yes!!!! They freeze beautifully. Set them on a sheet pan, uncovered, in the freezer for an hour or two to freeze individually. This will harden the centers so they’ll remain unblemished. Once frozen, transfer them into an airtight container. They’ll keep up to 2 months in the freezer.

Need them Gluten Free? These cookies also are delicious when made with a quality 1:1 all-purpose flour replacement, such as King Arthur Measure For Measure flour. The texture will be a little sandy.

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Fudgy Chocolate Thumbprint Cookies

Servings: 4 dozen 2″ cookies

Equipment

• Double boiler or microwave oven

Ingredients

Cookie Base

• 2 sticks regular margarine, no substitutes for best results
• 1 cup packed light brown sugar
• 2 teaspoons vanilla extract
• 3 cups all-purpose flour
• 1 teaspoon salt
• ¼ cup milk
• ½ cup semi-sweet or dark chocolate chips, chopped fine

Chocolate Filling

• 1½ cups semi-sweet or dark chocolate chips
• 2 Tablespoons shortening
• ¼ cup light corn syrup
• 2 teaspoons vanilla extract
• 2 Tablespoons water

Instructions

• Preheat oven to 350°. Line baking sheets with parchment paper or grease the sheets well.
• Using an electric mixer, cream the margarine and brown sugar until light and fluffy. Beat in vanilla.
• In a separate bowl, stir the salt into the flour. Add the flour to the creamed mixture alternately with the milk. Mix until just incorporated. Gently mix in the chopped chocolate. Don't overmix the dough. If you can, chill the dough for an hour or more.
• Roll dough into 1" balls and place on the cookie sheets at least 2" apart. (If the dough is a little crumbly when rolling, just roll in your hand a little bit longer.) Make a deep depression in each dough ball with either your thumb or with a wine cork. Don't break through the bottom of the dough. If the cookie cracks a little once depressed, just smooth the edges back together.
• Bake 10-12 minutes until the bottoms of the cookies are a little golden. Let cool on the sheet pan a few minutes, then pick up the whole parchment sheet and transfer to a rack or countertop. If not using parchment, just transfer the cookies to a rack or even to newspaper on the countertop. Cool completely.

Filling

• In a double boiler bottom, heat 1" of water to barely simmering. In the top half of the boiler, place chocolate chips, shortening, corn syrup, vanilla and water. Heat gently, stirring frequently, until completely melted and smooth. (You can also do this in the microwave, but be very careful to heat GENTLY.)
• Push your cookies together on the parchment – it makes filling easier. Place your whole double boiler on a hot pad beside the cookies. Using a soup spoon or another deep spoon, carefully fill the cookies. One scoop of the spoon will usually fill more than one cookie. You'll get the hang of it.
• Allow the cookies to cool for at least an hour to set the filling.

Notes

• This recipe will use one 12 oz. bag of chocolate chips.
• Hand chopping the chocolate chips for the cookie base is best, but you can use an electric chopper. Be careful to not chop them to dust.
• If the cookie loses a lot of it’s depression once baked, tap the depression again immediately upon removal from the oven.
• These cookies freeze beautifully. Simply lay them out on a sheet pan in a single layer and place them uncovered in the freezer for about an hour to preserve the unblemished filling. Transfer into an airtight container with wax paper or parchment between layers. The cookies will thaw quickly at room temperature.
• Leftover filling can be used for other things, like drizzling on top of coconut macaroons. 
• Need them Gluten Free? Substitute a 1:1 Gluten Free baking flour such as King Arthur Measure For Measure. The texture will be a little sandy, but still delicious!