Heat olive oil in a medium saucepan over medium-high heat. Add onion, bell pepper, and jalapeno. Season with salt and pepper, to taste. Cook until the onion and peppers become soft about 4-5 minutes.
1 tablespoon extra virgin olive oil, ½ medium yellow onion, 1 medium green bell pepper, 1 medium jalapeno, salt and pepper to taste
Stir in tomatoes, oregano, paprika, red pepper flakes, and water. Reduce heat to medium-low. Continue cooking, stirring occasionally, for another 4-5 minutes.
2 large tomatoes, ½ teaspoon dried Mexican oregano, ¼ teaspoon smoked paprika, ¼ - ½ teaspoon crushed red pepper flakes, ¼ cup water
Remove from heat and set aside to cool for a few minutes. Puree mixture with an immersion blender, leaving slightly chunky, or transfer to a regular blender or food processor and pulse a couple of times until blended.
Transfer salsa to a bowl. Stir in fresh lime juice and cilantro. Serve immediately or cover and refrigerate until ready to serve.