The partition of the Trieste Free Territory led to mass emigration by ethnic Italians living in Istrian coastal towns.

Neglected for more than two centuries, their commercial potential was poor and their industries obsolete, whilst maritime traffic and trade was strictly limited to local needs.

By August 1957, the Peter Klepec, a floating dredger had deepened the seabed along the northern shore of town, and concreting the area around the first berth began in December.

It was mainly companies trading in foodstuffs and timber - including, amongst others, the national Silo and Warehouses Administration, Emona, Slovenijales and Centroprom - that decided to co-finance or invest in the construction of the necessary infrastructure.

Freight passing through the port was for the most part hauled by road, with a minor portion travelling by rail to Kozina, and from there transported by truck to Koper, and vice versa.

During the early 1960s, outgoing maritime cargo, exports from the European continent, amounted to a mere 20 percent of total traffic, while the proportion of transit goods was similarly low.

The excellent results achieved in 1963 were also a consequence of the establishment of the first free zone, Luka Koper was able to provide a range of services for companies using the port.

This new orientation required the reorganisation of the company into six units: Handling, Warehousing, Timber, Maintenance, Joint Services and Luški dom.

Various problems pertaining to the co-ordination of rail and road transport between Koper and Kozina increased the demurrage costs of vessels, wagons and trucks.

Despite financial difficulties and the troublesome terrain, construction work gradually proceeded, and an auspicious and lavish inaugural ceremony on 2 December 1967 marked the commencement of operations on the 31-kilometre line between Koper and Prešnica.

As a result of favourable public opinion and excellent performance, the Koper line was officially incorporated into the national rail network.

In addition to petroleum derivatives, general cargo throughput also increased, which can mainly be attributed to the revival of Slovenian trade and commerce.

The 1980s were an extremely significant period in the development of Luka Koper; total throughput more than doubled, while the range of capacities were extended to those which the port has to this day.

The second half of the decade was characterised by considerable down-turns in raw timber and fruit throughput, which was due mainly to the more widespread introduction of containerisation.

And while petroleum derivates volume reached three-fold the level they had been in the early 1990s, the company actively capped the commensurate growth that was occurring in iron ore and coal traffic.

Although growth in container freight continued, it only increased by twenty percent over the decade, which for the most part was a consequence of the unstable political and economic situation experienced in many of the hinterland states during the early 1990s.

Nevertheless, Austrian clients—with 3.5 million tonnes, or a quarter of total throughput—still top the transit freight list, whilst trade with Italy, which now accounts for 15 percent of business, also grew rapidly.

During 2006, cargo throughput almost reached saturation level due to the limitations posed by the single-line rail link with the national network.

Over recent years the growth in container freight and vehicles has been of particular importance to the prosperity of Luka Koper, and shall remain among the company's key strategic development orientations over the coming decade.

In October 2023, the company initiated enforcement proceedings to recover damages from eight former board members, following a court ruling holding them liable for approving a financially detrimental investment in 2008.

Additionally, in November 2024, reports highlighted that one of these former members, Olga Franca, filed for personal bankruptcy in response to the substantial compensation demands.