Combine ¾ cup milk, ¾ cup cooled brewed coffee, and ½ teaspoon vanilla extract in a medium bowl. The liquid should have an even coffee color before the seeds go in.
Scatter ½ cup dry chia seeds into the liquid and mix thoroughly. At this stage, the mixture will look thin, with loose seeds moving through it.
Keep stirring for 30 seconds, leave the mixture undisturbed for 2 to 3 minutes, then stir thoroughly again. The developing gel coating will begin to hold the seeds throughout the liquid instead of letting them collect at the bottom.
Cover the bowl and chill for 6 hours or overnight, until the mixture reaches a pudding consistency. A spoonful should hold together rather than immediately flow back into the bowl.
Place ¾ cup plain Greek yogurt in a separate bowl. Its thick texture will form the creamy contrast to the coffee layer.
Beat ½ teaspoon vanilla extract and 1½ tablespoons honey or maple syrup into the yogurt, adding more sweetener to taste if desired. The topping should look uniform and taste gently sweet with a little yogurt tang.
Build alternating layers in jars or cups, beginning with coffee chia pudding, followed by sweetened yogurt and a light cocoa dusting, then repeat and finish with cocoa. Distribute the ½ tablespoon cocoa powder lightly so it doesn’t form dark, bitter pockets.
Serve the assembled pudding chilled. Each spoonful should combine thick coffee pudding, creamy yogurt, and a delicate cocoa finish.