In a medium bowl, whisk together eggs, onion, salt, and pepper. Distribute egg mixture evenly among cupcake liners. Add tomatoes, cheese, and basil to each cup.
Add water to the Instant Pot® and insert steam rack. Place steamer basket on steam rack. Carefully place cupcake liners in basket. Lock lid.
Press the Manual or Pressure Cook button and adjust time to 8 minutes. When timer beeps, quick-release pressure until float valve drops. Unlock lid.