An egg transfer system is provided. Such an egg transfer system includes a controller configured to receive a classification signal indicative of an egg classification status for each of a plurality of eggs carried by a flat. A transfer head assembly is in communication with the controller and is configured to remove a plurality of eggs from the flat. The eggs are grouped into at least a first and second subset based on the egg classification status. The controller is configured to direct the transfer head assembly to selectively release the first and second subsets separately based on the respective egg classification status of the eggs. An associated method is also provided.