Heat olive oil in a medium saucepan over medium-high heat. Add onion, bell pepper, and jalapeno and season with salt and black pepper, to taste. Cook, stirring occasionally, until the onion and peppers become soft, around 4-5 minutes.
Add tomatoes, Mexican oregano, smoked paprika, crushed red pepper flakes, and water. Stir to combine and reduce heat to medium-low. Continue cooking, stirring occasionally, for another 4-5 minutes.
Remove from heat and set aside to cool for a few minutes. Once slightly cool, puree mixture with an immersion blender, leaving slightly chunky.
Transfer salsa to a bowl and stir in fresh lime juice and cilantro. Season with additional salt and black pepper, if desired. Serve immediately or cover and place in the refrigerator until ready to use. Enjoy!