Argotti Botanic Gardens & Resource Centre initially started as two separate private gardens that were built in the early 17th century. One was owned by the Knight Don Emmanuel Pinto de Fonseca and the other by Bailiff Ignatius de Argote y Gusman. In 1741, after Pinto's election to Grandmaster, De Argote purchased Pinto's part of the garden and annexed it. During this period, the formal botanic garden was not yet established.

Argotti's history as a Botanic Garden originates as a physic garden that included herbs and medicinal plants. That was established around 1674 by the Knights of St John at Fort St Elmo near the Sacra Infermeria. When the British arrived in Malta, the medicinal plants and other botanical specimens were moved from St Elmo to Il-Mall in Floriana under the guidance of the Carmelite monk and Professor of Botany, Carolus Giacinto who was appointed Chair of Natural History by the University of Malta in 1805. After Giacinto died in 1855, the botanic gardens were relocated to Argotti Gardens by Professor Stefano Zerafa who was the Professor of Natural History at that time.

Zerafa's contribution to the gardens' botanical assets was very significant. Apart from writing the first account on Maltese flora, "Thesaurus of the Flora of the Maltese Islands", he is mostly remembered for the discovery and naming of our national plant, the endemic Cheirolophus crassifolius - the Maltese rock centaury.

The gardens enhanced their collections through contributions by leading Maltese botanists prominent amongst which were Count Alfred Caruana Gatto and Professor John Borg. This resulted in notable collections of indigenous and Mediterranean flora, cacti and succulents. In 1945, the wife of late Prof. Borg contributed his world-famous private cacti and succulent collection to the University of Malta, and this was housed at the Argotti.

The gardens passed over to the Department of Agriculture in 1973 after 150 years of University tenure. The inner part was returned to the University of Malta in 1996, and since then the University embarked on a number of restoration works, including the herbarium.