The Santa Cruz Cathedral not only happens to be one of the oldest churches in Cochin, but also in the whole of India. Counted as one of the heritage edifices of Kerala, this church is visited by tourists the whole year round. It was built by the first Portuguese viceroy, Francesco de Almeida, when he arrived in Kochi way back in 1505. On 3 May that year, during the feast of the "Invention of the Holy Cross", the foundation stone of this church was laid and upon completion, it was christened as Santa Cruz Cathedral.

Later on, when the Dutch conquered Cochin in 1663, they ruined all Catholic establishments except this particular cathedral and the famous church of St. Francis. In those days, the Santa Cruz Cathedral was used as an armory. It was, however, later shattered in 1795, after the British took over the city. An elaborate granite pillar of this monumental cathedral was what remained after the destruction of the Santa Cruz Cathedral. The pillar is still kept on the southeastern corner of the present Basilica.