Set oven to 350°F, rack in the middle.
Blend tomatoes and onion in a food processor until smooth. Make 2 cups.
Deseed and mince two jalapeños, set aside; mince one with seeds, set separately.
Rinse rice under cold water until clear, about 1.5 mins. Drain well.
Heat olive oil in a 12-inch oven-safe pan over medium-high until a few grains of rice sizzle.
Add rice, cook stirring until golden, 6-8 mins.
Reduce heat to medium, add garlic and seeded jalapeños, stir until fragrant, 1.5 mins.
Add tomato-onion puree, broth, tomato paste, and salt. Bring to boil.
Cover pan, transfer to oven, bake 30-35 mins, stir well at 15 mins.
Stir in cilantro and reserved jalapeño with seeds.
Serve with lime wedges.