Aspects of a method and system for physical layer control of low latency state transitions for energy efficiency. In this regard, a determination may be made to reconfigure a network device from an energy saving mode of operation to a higher performance mode of operation. A first portion of the network device may be reconfigured prior to sending an indication of the reconfiguration to a link partner, and a remaining portion of the network device may be reconfigured after sending the indication. The link partner may begin reconfiguration from an energy saving mode of operation to higher performance mode of operation upon receiving the indication. The energy saving mode may comprise a low power idle (LPI) or a subset PHY mode. The reconfiguration may comprise allocating memory to, and/or de-allocating memory from, buffering received and/or to-be-transmitted data.