In a food processor, add in lime juice, orange juice, thyme, cinnamon, garlic, ginger, soy sauce, brown sugar, jalapeno, and apple cider vinegar. Blend well.
Place chicken in the instant pot and top with quartered onions and tomatoes. Pour mixture over the top and toss well. Top with salt and pepper.
Set Instant Pot or Pressure Cooker to manual high pressure for 20 minutes. Once it's done counting wait 5 minutes and release pressure.