Fort Cochin has a good range of restaurants, many of them in guesthouses and heritage buildings.
Kashi Art Cafe on Burgher Street is the most popular spot in Fort Cochin, and the chocolate cake is the main reason. Breakfast and lunch are excellent, though the menu is not very flexible. The atmosphere is relaxed, with art on the walls and good music. It gets busy, so go early.
Dal Roti on Lily Street serves excellent North Indian food at reasonable prices. The dal makhani and the parottas are both very good. Simple setting, friendly service.
For fresh seafood, walk down to the Chinese fishing nets at sunset and buy fish directly from the fishermen. Several small stalls nearby will cook it for you on the spot for a small fee. It does not get fresher than this.
The Kerala thali is worth seeking out at one of the smaller local restaurants in Ernakulam. A banana leaf loaded with rice, sambar, rasam, aviyal and fish curry is a proper Kerala meal, and you will pay very little for it.