In S1 E49* So close, yet so Fafetch'd we have a PokéDex entry that clearly indicates Pokemon are eaten:
Farfetch'd, a wild duck Pokémon. Farfetch'd makes a delicious meal, especially when cooked with leek. Because of this, Fafetch'd is nearly extinct.
Early in the season, on E15 "Pokémon Shipwreck", we see the stranded group daydream about eating Magikarp, to the point that Meowth actually tries to eat one but breaks his teeth on Magikarp's armored scales.
Filleted, fried, marinated! The only thing Magikarp is good for is a meal!
Much later in the anime, in the Diamond and Pearl series, E144 An Egg Scramble! shows people drinking MooMoo Milk and eating ice cream made from it. It's generally known that MooMoo Milk comes from Miltank:
In the games, you get the milk on MooMoo Farm, and have to help heal their Miltank. In the manga, Miltank Melee, MooMoo Farm is also featured, and also includes a sick Miltank that starts producing milk again once healed. The key word here is farm.
There's also ranches, such as Laramie Ranch, but the show doesn't indicate that any of the cattle-type Pokémon there are eaten, instead their raised to be stronger for trainer battles.
As I was looking into this details (some of which are pretty fresh to me, as I'm rewatching the series with my oldest child), I found that several of these cases are covered in this Bulbapedia article's section "Human's eating Pokémon" and "Food produced by Pokémon".
However, most of the concepts of Pokémon being food go away as the games, anime and manga go on. Those early episodes also included other oddities, such as a variety of giant Pokémon (in several episodes), and references to real-world locations (such as Melvin the magician that wants to perform in Las Vegas) and historical figures that are generally phased out.
*Some numbers are different than those listed on sites like Bulbapedia, I'm using the numbering used by Netflix, which is where I'm actually watching the show.