The Mercado Central is the place to eat if you want to eat cheaply and well. The vendors inside serve pupusas — El Salvador's stuffed corn flatbread — along with tamales, riguas (fresh corn pancakes), and simple comidas corrientes throughout the day. It's loud, crowded, and efficient.
The market is also a good place to buy locally grown coffee, which sells at prices that reflect the actual source rather than the markup of tourist-oriented shops. Head there in the morning when activity is at its peak. Central Santa Ana, adjacent to the historic district.