Combine peanut butter, cocoa powder, honey, coconut oil, butter, and vanilla bean paste in a saucepan over low heat; cook, stirring constantly, until melted and smooth, 3 to 5 minutes. Remove saucepan from heat and transfer peanut butter mixture to a bowl.
Refrigerate mixture, stirring every 5 minutes, until truffle mixture is firm yet sticky and soft enough to shape, about 15 minutes.
Pour coconut flakes into a bowl. Drop truffle mixture, about 1 teaspoon per truffle, into coconut and roll to coat. Refrigerate until firm, about 15 minutes.