Co-operative Bulk Handling contracted CPB Contractors to design and construct 10 new steel cells to provide an additional 60,000 tonnes of storage capacity to the terminal along with upgrades to conveyors, grain elevators, and ship loaders. Dust control systems, mechanical instrumentation and electrical control systems were also enhanced.

The project commenced in July 2004 and was completed in September 2006 at a cost of $122 million.

The Albany Port Authority won the national Lloyd's Port of the Year award in 2006 for its development of new technology used to restore degraded load-bearing concrete piles without disrupting cargo handling activities.

On 11 April 2007, the world’s first purpose-built Albanymax ship was launched at Kurashiki in Japan. An Albanymax ship is the largest vessel which can be loaded at Albany’s wood chip berth (Berth 6). She was built by Mitsui specifically for the wood chip trade between Albany and Japan.

On 13 September the Port hosted the ‘Great White Fleet’ centenary re-enactment in conjunction with a Port Open Day, which attracted over 5,000 visitors.

The bulk carrier 'Atlantic Eagle' was grounded on Maude Reef, outside of King George Sound on 15 July. The Australian Transport Safety Bureau described the response to the incident as “timely and well-managed”.

The ship had lost steering and was listing but there was no impact on the local environment.

The ship was charged a $250,000 fee to allow its damaged rudder to be dropped on the sea bed, creating a dive site and funding for community’s benefit.

Exports of Biomass Pellets commenced in September, with 26,531 shipped in 2009/10. Albany became the first port in Australia to export this product.

The process of producing wood pellets involves making an energy-dense wood pellet from sawmill residue and woodchips milled to less than 5mm in size.

Captain Sean Bolt was Harbour Master from 2011

A new tug licence was negotiated with Svitzer Towage, which saw two new tugs at the Port, the ‘Koona’ and the ‘Karoo’.

Both tugs were built in 1991.

Gross Tonnage: 307 t, Deadweight: 291 t, Length Overall x Breadth Extreme: 31m × 11.13m.

Delivered in August 2012, Pilot Vessel ‘Mokare’, of ORC 15.6 design, 22 tonne, moulded FRP carbon composite and length of 16m, was built in 2012.

A public competition naming the vessel was won by Mr Greg Smithers.

'Mokare' was a Menang man. With the arrival of Major Edmund Lockyer in the brig 'Amity' in 1826, he acted as a guide and mediator between the two cultures. 

The ‘Mokare’ replaced the PV ‘George Vancouver’.

Albany, Bunbury and Esperance Ports amalgamated to form Southern Ports Authority on 1 October 2014.