Prepare the oven and pan: Position an oven rack in the top third of the oven and preheat to 425°F / 220°C. Lightly coat a 9-inch pie dish with cooking spray.
In a small bowl, whisk together the reserved liquid from the pinto beans and the tomato paste until smooth.
Sauté the aromatics: Heat the olive oil in a large skillet over medium-high heat.
Add 2 cups (480 ml) of the diced onion, cover, and cook for 4 minutes, stirring occasionally, until softened.
Stir in the chili powder and cook for 10 seconds until fragrant.
Simmer the chili filling: Pour the tomato paste mixture into the skillet, along with 1 cup (240 ml) of the chopped tomatoes, the rinsed beans, and 1½ cups of water.
Bring the mixture to a simmer, then reduce the heat to low.
Let it simmer uncovered for 6 minutes, allowing the flavors to meld and the chili to thicken.
Season with salt and pepper to taste.
Mix the cornbread batter: While the chili simmers, combine the cornbread mix, ⅓ cup of Greek yogurt, the egg, sugar, and 1 tablespoon (15 ml / 0.5 fl oz) of water in a medium bowl.
Stir until just combined—do not overmix.
Assemble and bake: Spread the pinto bean chili evenly in the prepared pie dish. Gently pour the cornbread batter over the chili, using the back of a spoon to spread it to the edges.
Bake for 10-12 minutes, or until the cornbread topping is set and a beautiful golden brown.
Make the fresh salsa: While the pie bakes, finely chop the remaining ½ cup of onion and combine it in a small bowl with the remaining ½ cup of tomatoes.
Season the salsa with a pinch of salt and pepper.
Serve and enjoy: Let the shepherd’s pie cool for a few minutes before dividing it among shallow bowls.
Serve warm, topped with a dollop of the fresh tomato salsa and the remaining 1 cup (240 ml) of Greek yogurt.