Add the diced apples, honey, cinnamon, cloves, nutmeg, vanilla, and water to a small saucepan.
Simmer the apple mixture over medium heat for 5 to 10 minutes, until the apples have softened.
Remove the apples from heat and set aside to cool completely.
Mix ½ cup of Greek yogurt with the peanut butter and honey until combined.
Add a layer of plain Greek yogurt to a glass or small bowl, followed by a layer of stewed apples, granola, and then peanut butter yogurt. Repeat the process with the remaining ingredients and a second glass.
Top off the parfaits with an extra drizzle of honey, if desired, and serve.