Preheat the oven to 375°F (190°C) and line baking sheets with parchment paper or silicone mats.
In a large bowl, beat together the creamy peanut butter and softened butter until smooth.
Add the white sugar and brown sugar to the bowl and beat until the mixture is light and fluffy.
Mix in the eggs one at a time, then stir in the vanilla extract until combined.
Add the all-purpose flour, baking soda, and salt; stir until a soft dough forms that is not sticky.
Measure about 2 tablespoons of dough and roll into a ball. Place dough balls 2 inches apart on the prepared baking sheets.
Bake for 9–11 minutes, until the edges are set and the centers are still slightly soft.
Immediately after removing the cookies from the oven, press the back of a teaspoon into the center of each cookie to create an indentation.
Spoon about 1 teaspoon of grape jelly (or chosen flavor) into each indentation and allow cookies to cool on the sheet until set.