Preheat the oven to 350°F (175°C).
Arrange the mini phyllo shells in a single layer on a parchment-lined baking sheet.
Bake the empty shells for 5 minutes until lightly golden and crisp. Remove from oven and cool for 2 minutes.
In a small mixing bowl, combine the red pepper jelly and finely chopped dried cranberries. Stir vigorously to incorporate. If the jelly is too firm, microwave for 15 seconds to soften.
Whisk the softened cream cheese with the cracked black pepper until smooth and aerated.
Transfer the cream cheese to a piping bag or use a small spoon to deposit approximately 2 teaspoons into each phyllo shell.
Top the cream cheese layer in each shell with approximately 1 teaspoon of the cranberry pepper jelly mixture.
Garnish the finished cups with orange zest and minced chives.
Serve immediately at room temperature.