In 1912, he was appointed artistic director of the Augusteo Orchestra, Rome, later renamed l'Orchestra dell'Accademia Nazionale di Santa Cecilia, a position he held until the end of the Second World War. Since this was then, like now, the leading symphony orchestra position in Italy, it aroused the envy of several rivals.
After the liberation of Rome on 4 June 1944, Molinari was contested by the public, in particular during two concerts held on 9 and 12 July, for his involvement with the Fascist regime. He had to suspend the performance and, since then, he was able to conduct in Rome the Orchestra of the Theatre of Opera only.
In 1945, he arrived in Palestine and conducted the Israeli Philharmonic Orchestra, then became its musical advisor. The performance of the Korngold violin concerto with David Grunschlag as soloist was critically acclaimed
Composer Robert Starer tells of his experience as young harpist in the Palestine Orchestra in the 1940s:
I sat behind [my] harp, glanced at the most intricate harp part I had ever encountered, and looked with heavily beating heart at the conductor, Bernardino Molinari, a fine, experienced maestro. He must have sensed how I felt, for he gave me every single cue and somehow helped me to get through the first movement without any noticeable mishap…\"
- Ottorino Respighi: Pini di Roma, Augusteo, Rome, 4 December 1924
- On 15.12.1947 Molinari directed Josef Tal's Exodus premiere with the Philharmonic Orchestra in Tel-Aviv.