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 by the Allied Troops of June 4th 1944, Molinari was contested by the public, in particular during two concerts held on July 9th and 12th, 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. 
Composer Robert Starer tells about a musical experience he had as Palestine Orchestra's young harpist in the 40s:
"…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.
- Antonio Vivaldi: Four Seasons, Parlophone/Cetra 1942
- Ottorino Respighi: Fontane di Roma, Odeon, ca.1942
- Mucci, E.: Bernardino Molinari. Lanciano, 1941.
- Grove Dictionary of Music, Fifth Edition.