In 1890, after the death of the founder of the museum, the city council appointed the staff meeting of the high school as curators of the collection.

In 1906, the museum collection was moved to Museo del Ateneo, where it stayed until 1944, when they became part of the recently inaugurated Museo Provincial de Bellas Artes (Provincial Museum of Fine Arts), organized by Félix Merino and M. Lluïsa Serra.

Mahón City Council ceded Can Mercadal palace, home to the House of Culture and currently the public library, where the new museum was placed in November 1948.

From 1953 to 1967, under the direction of M. Lluïsa Serra, the collection continued increasing with the acquisition of artwork and donations from Menorcan painters, and important tasks of documentation and diffusion were carried out too.

In this period the museum also kept archaeological materials from important sites that were under research in that time, such as Naveta d'Es Tudons, Rafal Rubí naveta, the settlement of Talatí de Dalt, Fornàs de Torelló and Illa del Rey basilicas, among others.

Five years later, in 1980, a building belonging to Mahón city council was donated to the State, which was the old Franciscan convent, which became the new and permanent home to the museum.

Since 2007, a team of archaeologists from the museum carry out archaeological research at the site of Cornia Nou, which is a Talayotic settlement located near Mahón which counts with two layouts and related buildings.

In the ground floor of the convent there was the reception, the chapter house, the kitchen, the pantry, the cellar, the refectory and the schools of grammar and philosophy.

Periodically the museum publishes scientific archaeological work, collection guides, catalogues of temporary exhibitions and publications for educational purposes that offer the opportunity to learn about the History of the island.

For schools, the museum prepares visits focusing on one or several periods, and designing the routes for each educational level or the needs of students.

Moreover, Museu de Menorca organises activities addressed to several types of groups, including workshops for children, gymkhanas, nights at the museum, specialised visits, lectures and presentations of artefacts.