Add raspberries and ¼ cup agave to a food processor or blender and blend until smooth. Transfer to a bowl and set aside.
Clean out the food processor and add blueberries, ¼ cup of agave, and blend until smooth. Transfer to another bowl, cover with plastic wrap, and keep in the refrigerator until ready to use.
Layer one-third of the popsicle mold with raspberry puree. Freeze for 1 hour.
In a small bowl, combine the remaining ¼ cup of agave and yogurt. Use yogurt mixture to layer the next one-third of the popsicle. Freeze for another hour.
Add the final blueberry puree layer to the mold, insert popsicle sticks, and freeze for another 2 hours or until completely frozen.