You can only give the chocobo color fruits while they're stabled. Feed the fruits in the recommended order so that you avoid bottoming out or topping out any of the RGB values. As you feed the fruits, you might see multiple messages about the plumage beginning to change color. Feed all the fruits, then leave the chocobo alone for six hours.

After the time has passed, the chocobo will have changed color. If it's not the color you were aiming for, some of the RGB RNG went out of the tolerable ranges for the color you wanted. Repeat the process using the new color as a starting point. You'll need fewer fruits because the new color should already be within a couple shades of your target color.