Preheat oven to 350° Fahrenheit. Line a muffin pan with 12 cupcake liners. Set aside.
In a medium bowl, whisk together flour, almond meal, baking powder, and salt. Set aside.
In a large bowl, whisk together melted butter and sugar. Add in eggs, Greek yogurt, milk, vanilla extract, and almond extract. Whisk until combined.
Using a sieve, sift the dry mixture into the wet mixture. (This is important to remove any clumps). Gently whisk until smooth.
Divide the batter into the 12-cup lined muffin pan, filling each cup about 3/4 of the way full. (Tip: use a large cookie scoop for easier measuring).
Bake for about 18-22 minutes, or until a toothpick inserted into the center comes out clean. Place cupcakes on a wire rack to cool.
Meanwhile, make the cherry filling. Place pitted, coarsely chopped cherries in a bowl. Drizzle with honey and toss with a spoon to coat. (If making cupcakes ahead of time, stop at this step and read the storage tips in the Notes section).
Once the cupcakes are cool, use a small spoon or knife to core a hole out of each cupcake, about 1 inch in diameter, reaching about 2/3 of the way down the cupcake. (Don't go too deep, or the filling will seep out). Spoon cherry filling into each cupcake's center.
Lastly, top with whipped cream or frosting and decorate as desired. Then, serve!