Prepare the watermelon pureé: Cut fresh watermelon flesh into chunks and blend in a blender or food processor until smooth. Measure out 1 cup of the pureé and set aside.
Preheat the oven to 350°F (175°C). Line a muffin tin with paper cupcake liners. In a small bowl, measure the watermelon pureé and set aside.
In a large mixing bowl, cream together the softened butter and granulated sugar using an electric mixer on medium speed until light and fluffy, about 2-3 minutes. Observe the mixture turn pale and increase in volume.
Add eggs one at a time, beating well after each addition. The batter should become smooth and slightly thickened. Smell should be sweet and buttery.
In another bowl, whisk together the dry ingredients: flour, and optional watermelon seeds. Gradually add the dry mixture to the wet mixture alternately with milk, starting and ending with the dry ingredients. Mix gently with a spatula until just combined. The batter will be slightly thick but pourable, with small specks of seeds if used.
Gently fold the watermelon pureé and vanilla extract into the batter until evenly incorporated. The mixture should be uniformly pink with visible seed specks.
Spoon the batter into the prepared cupcake liners, filling each about two-thirds full. Place the tin in the oven and bake for 20-25 minutes, or until a toothpick inserted into the center comes out clean and the tops are lightly golden.
Remove the cupcakes from the oven and let them cool in the tin for about 10 minutes. Then, transfer them to a cooling rack and allow to cool completely before serving. The cupcakes should be moist, with a tender crumb and small seed specks visible throughout.
