In a medium bowl, whisk together the Greek yogurt, honey, and vanilla extract until smooth.
Pour the mixture into an ice cream maker and churn according to the manufacturer's instructions until thick and creamy (about 20-25 minutes).
If you don't have an ice cream maker, pour the mixture into a shallow dish and freeze for 1 hour. Stir vigorously with a fork to break up ice crystals, then freeze for another 2-3 hours, stirring every 30 minutes, until firm.
Scoop the frozen yogurt into the waffle cones.
Add optional toppings immediately and serve.
Tips
For a fruitier flavor, swirl in 1/2 cup of fruit puree before freezing.
Store any leftover frozen yogurt in an airtight container in the freezer for up to 1 week.
Let the frozen yogurt sit at room temperature for 5 minutes before scooping if it's too hard.