Born into a family of musicians, he studied the horn and cello and graduated in cello at  Milan Conservatoire under Rocco Filippini.
He soon began his career as a brillant cellist. He became  first cello to the Orchestra of  Teatro Comunale, Bologna, and was regularly invited to perform at important international festivals together with world famous soloists such as Salvatore Accardo, Yuri Bashmet, Giuliano Carmignola, Bruno Canino, Bruno Giuranna, Paul Tortelier and Sandor Vegh.
 
In the Eighties Marco Boni was among the founders, and solo cello, of the Chamber Orchestra I Virtuosi Italiani. He conducted I Virtuosi successively in numerous concerts in Italy, Switzerland and Spain and recently at the Turku Festival in Finland. With the same orchestra he released for Chandos the first world recording of Nino Rota’s Piano and orchestra concerts.
 
In 1987 he renewed a long-standing contact with Sergiu Celibidache, who had taught him the rudiments of orchestral conducting when Marco was only eleven. Marco Boni’s conducting career reached a significant turning point in 1994 when, after a successful tour of some major Italian cities, he became Principal Conductor of the Amsterdam Concertgebouw Chamber Orchestra, (founded by the elites of the prestigious Royal Concertgebouw Orchestra).
 
In the same year he made his debut at Teatro Comunale of Florence with the Chorus and Orchestra of  Maggio Musicale Fiorentino, and he was on  tour in Italy with the Scottish Chamber Orchestra together with the soloist Giuliano Carmignola. The tour culminated at the Rovereto Mozart Festival.
 
With the Concertgebouw Chamber Orchestra he has toured France, Spain (12 tours), Italy (6 tours), Belgium, India, Japan (2 tours), Germany,Switzerland and more recently Portugal with the pianist Maria Joao Pires, obtaining everywhere unanimous acclaim.
 
His first recording of Mahler’s arrangements of the quartets “Death and the Maiden” by Schubert and the quartet Op. 95 by Beethoven received acclaim from the critics all over the world, rated by the BBC Music Magazine as “absolutely,the best recording available of these works .” obtaining a vote of five star for the astonishingly precise interpretation of the works.
 
With the Concertgebouw Chamber Orchestra, four recordings of works by Haydn, Mozart, Mendelssohn, Schubert and Tchiaikovsky were released, accompanied by flattering reviews in worldwide musical magazines.
 
The latest recordings include a CD of Vivaldi and Bach for the label Victor with the Filarmonici of the Bologna Teatro Comunale. And a double CD entirely dedicated to Giuseppe Verdi was released after the successful tour in India with the Chorus and Orchestra of Teatro Regio di Parma and the bass Michele Pertusi.
 
Recently he made two tours respectively in Italy and Spain with the orchestra Concertgebouw and Misha Maisky. A concert has taken place at the hall of Concertgebouw Amsterdam, which was recaptured and broadcast by Japanese television NHK and has been broadcasted in Italy on Sky Classic Channel.
He conducted Orchestra Regionale Toscana and Swingle Singers. The remarkable concert has been broadcast on Rai Radiotre.
Marco Boni and Wiener Kammerorchester achieved a great success with the concerts in Italy and Spain and after a performance at the Konzerthaus in Vienna a series of concerts in Italy, Spain and Vienna has been scheduled.
In the summer of 2010, Marco Boni conducted a series of symphonic concerts with the Orchestra of Teatro Comunale di Bologna; with the same Orchestra the concert for the Mahler celebrations 2011, the opera Carmen and two ballet  productions  with  Maggio Danza company.  The ballet Le Sacre du Printemps by Stravinsky has been scheduled with the same orchestra.
Since the autumn of 2010,  he started  his collaboration  with Imola International Piano Academy and he  became  permanent  teacher of conducting.
 
After 18 years of cooperation with the Concertgebouw Chamber Orchestra in june 2012 he has been appointed unanimously  Onorary Conductor.