Cheesy Thumbprint Cookies with Red & Green Pepper Jelly

If you’re looking for a holiday appetizer that feels a little unexpected but still completely festive, these Cheesy Thumbprint Cookies with Red & Green Pepper Jelly are it. They’re buttery, savory, and packed with sharp cheddar, with a sweet-spicy pepper jelly center that adds just the right amount of contrast.

They’re perfect for holiday parties, cheese boards, and cookie swaps when you want something savory to balance out all the sweet treats. Plus, the red and green jelly gives them a subtle Christmas look without feeling gimmicky.

Why You’ll Love These Cheesy Thumbprint Cookies

Easy to customize with different pepper jelly heat levels

Savory and festive, a refreshing break from sweet holiday desserts

Made with sharp cheddar for bold, cozy flavor

Perfect for holiday appetizer spreads and cheese boards

Make-ahead friendly for stress-free entertaining

Ingredients You’ll Need

For the Red & Green Pepper Jelly

Red bell pepper: Adds natural sweetness and creates the base for the red jelly.

Green bell pepper: Brings freshness and color contrast for the green jelly.

Red chili pepper: Adds gentle heat to the red jelly without overpowering it.

Jalapeño pepper: Gives the green jelly a little more kick and depth.

Apple cider vinegar: Balances the sweetness and helps the jelly set properly.

Coconut sugar: Sweetens the jelly while adding a subtle caramel note.

Pectin: Helps the pepper mixture thicken into a spoonable jelly as it cools.

For the Cheesy Cookies

Unsalted butter: Creates a rich, tender base for the cookies.

Egg: Binds the dough and gives structure.

Coconut sugar: Adds just a hint of sweetness to balance the sharp cheese.

Arrowroot starch: Helps keep the cookies tender rather than crumbly.

All-purpose flour: Forms the structure of the dough.

Milk: Adds moisture so the dough comes together smoothly.

Sharp cheddar cheese: The star of the recipe. Sharp cheddar is essential for bold, savory flavor.

Ingredient Swaps & Variations

Want more heat -> Add extra jalapeño or chili pepper to the jelly.
Only one color jelly -> Use one full bell pepper and adjust spice peppers to taste.
Different cheese -> Sharp white cheddar works well, but avoid mild or soft cheeses.
Mini cookies -> Make smaller dough balls for appetizer platters.

How to Make Cheesy Thumbprint Cookies (Step-by-Step)

Step 1: Make the pepper jelly

For the red jelly, add the red bell pepper and red chili pepper to a small blender with part of the apple cider vinegar and blend until nearly smooth. Transfer to a small saucepan and stir in half of the coconut sugar and pectin.

For the green jelly, add the green bell pepper and jalapeño to the blender with the remaining vinegar and blend until nearly smooth. Transfer to a second saucepan and stir in the remaining sugar and pectin.

Bring both mixtures to a boil and cook until they reach 220°F. Remove from heat and allow to cool to room temperature. The jelly will thicken as it cools.

Step 2: Make the cookie dough

In a mixing bowl, beat the softened butter, egg, and coconut sugar until combined. Small specks of butter are completely fine and add flavor.

Stir in the arrowroot starch, then gently fold in the flour until just combined. Add the grated sharp cheddar cheese and milk, mixing gently until the dough comes together. Cover and refrigerate for 30 minutes.

Step 3: Shape and bake

Line a baking sheet with parchment paper. Shape the dough into evenly sized balls and place them on the baking sheet. Use your thumb or a teaspoon to gently press an indentation into the center of each cookie.

Bake until lightly golden and set.

Step 4: Fill the cookies

Remove the cookies from the oven and immediately re-press the indent if needed. Transfer to a cooling rack and fill each cookie with red or green pepper jelly.

Helpful Tips Before You Bake

These cookies are simple, but a few small details make a big difference. Always use sharp cheddar for the best flavor. Be careful not to overmix the dough, as that can make the cookies dense or rubbery instead of tender.

When making the indent, press gently. Pressing too deeply can cause thin bottoms that may overbake. For even baking, keep all dough balls roughly the same size. Allow the pepper jelly to cool completely before filling so it sets properly inside the cookies.

Storage & Make-Ahead Tips

Store the filled cheesy thumbprint cookies in an airtight container in the refrigerator for up to 3 days. Because of the pepper jelly filling, refrigeration helps keep the cookies fresh and prevents the centers from becoming too soft.

If you want to make these ahead, you can bake the cookies and prepare the pepper jelly separately up to several days in advance. Store the unfilled cookies in an airtight container at room temperature and keep the pepper jelly refrigerated. Fill the cookies shortly before serving for the best texture and appearance.

For serving, allow the cookies to sit at room temperature for about 15–20 minutes so the texture softens slightly and the flavors shine.

Freezing is not recommended once the cookies are filled, but the unfilled baked cookies can be frozen for up to one month. Thaw completely before adding the pepper jelly.

Frequently Asked Questions

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