Press wonton wrappers into a lightly greased mini muffin tin. Bake at 375 degrees F. until cups are crispy and browned around the edges, 8-10 minutes.
Simultaneously, add bacon strips and jalapenos to a baking sheet and bake until bacon is crispy and jalapenos are blistered, about 18-20 minutes. Remove and let cool briefly (transfer bacon to a few paper towels to drain grease).
In a medium bowl, stir together Greek yogurt, cheese, chives, garlic powder, salt, 1 roasted jalapeno (seeded and diced) and 3 strips of crunchy bacon, chopped.
Chop the remaining bacon for a topping on each cup and seed the remaining jalapenos. Slice the jalapeno into thin strips for a garnish.
When ready to serve, spoon the filling into each wonton cup. Top with a sprinkle of crumbled bacon and a jalapeno slice.
These can be made well in advance, but don’t assemble the cups until right before serving so the wonton cups stay crispy.