At the time of its commissioning in 1888, the Mormugao Port comprised of 3 berths along with a breakwater having a length of 358 meters. As the years rolled by, the infrastructure slowly kept growing. By 1922, Berths 4 and 5 were built and the breakwater was extended to its present length of 522.40 meters. A mole of 270 meters was added.

With the emergence of mining as a major industry in Goa, a Master Plan was evolved by the Portuguese for the development of Mormugao Port as an iron ore terminal, envisaging “dedicated berth fitted with Mechanical Ore Loading Plants, provided and financed by various iron ore exporters.” In accordance with this, in 1959 M/s Chowgule & Co. Pvt. Ltd., was permitted to set up Asia’s very first Mechanical Ore Handling Plant at Berth No.6, with a capacity of 1000 tph. Berth 7 was constructed as an adjunct to it. The Liberation of Goa on December 19, 1961 marked the end of an epoch in Goan history.
Mormugao Port, went through a fair amount of change as the emphasis shifted to development of infrastructure. A couple of years after liberation, the port was delinked from the Railway management. The main railway section from Vasco da Gama to the border of Goa was transferred to the Southern Railways. The Port however, operated its own railway system between Vasco da Gama interchange point and the harbour area.
From 1948 onwards the iron ore traffic gained importance. The Japanese were rebuilding their nation and Goan iron ore was fated to play a key role in the Japanese industrial renaissance. Japan preferred Goan Iron ore for its expanding steel industry on account of price consideration and other logistics. The Port of Mormugao was now poised for a dramatic growth. It would no more be a sleepy port importing table wines from Portugal and exporting oil cakes from Hubli.
Others avenues had earlier been opened by enterprising foreigners. Josephine Hougaz was one such an ethnic Syrian holding a US passport. She introduced Goan cashew nuts to American chocolate makers. Wall Street had crashed. The year was 1929,for almonds and walnuts, until then the preferred fillings for American chocolate and pastry makers, had reached levels that were beyond most of their consumers. But cashew nuts, though subject to considerable sea freight additional for importers, were in comparison cheap but nutritious and tasty American confectioners took to Goan cashew nuts in the year of the wall  street crash.
The exploitation of iron ore mines in Goa on a commercial scale since 1947, brought about revolutionary changes in the pattern of Mormugao Port traffic. The level of  traffic at the port rose to over 2.78 lakhs tonnes  in the year 1953. In the  years that followed, the traffic grew by leaps and bounds reaching the mark of 6.4 lakh to 14.8 million tonnes in 1973-74. Today, the iron exported through Mormugao constitutes 39 per cent of the total iron ore exports from India, and the port occupies a prestigious position amongst the Major Ports of the country.
The growth of traffic accentuated the inadequacy of the available port facilities but it offered new opportunities to daring entrepreneurs.
In 1959, Chowgule & Co. Pvt. Ltd., obtained a concession from the Portuguese government and set up a Mechanical Ore Handling Plant with a handling capacity of 10,000 tonnes per day. It was, it is claimed, the first of its kind in Asia.
The  declaration of Mormugao as a Major Port in 1964 was a milestone in the annals of its history as it joined the ranks of the country’s ten major Ports. The Port  administration could now embark upon a sustained development programme as its newly formed Board of Trustees was empowered to take major decisions financial or otherwise.
With the rise of Brazil and Australia in recent times as aggressive ore exporters, the mineral ore industry today was seeing a sea of changes in iron ore market.
In 1965 therefore, a Perspective Plan was drawn up by a reputed firm of consulting engineers, seeking to develop Mormugao Port systematically for providing deep waters and high capacity loading, particularly in relation to iron ore exports, which needed to be competitive in the international arena by reducing the transportation cost.
As a first  step in that direction, a 20-year perspective plan for the port development was prepared in February 1965, by the consulting engineering firm of Randal, Palmer & Tritton. Thereafter, in February 1968, HOWE ( India) Pvt. Ltd. were appointed to prepare the design study for the establishment of a modern mechanical ore handling facility for the port within the framework of the perspective plan. As a follow-up on the report by HOWE (India) Pvt. Ltd. a mechanized ore handling facility for receiving, stockpiling, reclaiming, weighing, sampling, and ship-loading of 12 million tones of iron ore annually was installed and commissioned in 1979. The rated loading capacity of the ore handling system was of the order of 8,000 tones per hour. The dredging of the channel and berths was carried out to permit the loading  of 60,000 dwt. ore carriers initially. Barge unloaders and rail wagon tippers were provided for quicker and more efficient handling of incoming ore.

Major developments of the Port were taken up only after it became a Major Port. A number of developmental projects were implemented under the various Five Year Plans of the Government of India. Consequently, a dedicated mineral oil berth, berth No. 8 was constructed in 1976. Later on as the general cargo traffic was gradually picking up in the Port, a number of schemes were implemented with a view to augment the general cargo handling facilities at the Port. Two multi-purpose general cargo berths, berth No.10 and No. 11  having draft of 11.00 mts and 12.50 mts were constructed and  commissioned in 1985 and 1994 respectively. Meanwhile the Mechanical Ore Handling Plant installed in 1959 at Berth No. 6 was de-commissioned in 1992 due to obsolesce. The age old berths 1 to 3 were leased out to a private company, Western India Shipyard Ltd, for installing a modern ship repair facility, which was commissioned in 1995. In 1997, the metre guage railway of the Port linking to the south Central Railway was converted to broad guage. By this, the Mormugao Port is now accessible for any part of the country through the broad guage railway system.