The Montecristo brand was created in 1935 by Menende, Garcia and Cia, then the owners of the popular H. Upmann brand of cigars. Having just purchased the H. Upmann marque from J. Frankau & Co., Menéndez and García decided to produce their own subset of the regular H. Upmann line, called the H. Upmann Montecristo Selection.

The name for the brand was inspired by the Alexandre Dumas novel The Count of Monte Cristo, which was supposedly a very popular choice among the torcedores (cigar rollers) in their factory to have read by the lector on the rolling floor.

On the insistence of the John Hunter firm of Great Britain (which would later merge with J. Frankau & Co. to form Hunter & Frankau, Britain's sole importer of Cuban cigars to this day), the name was shortened to simply Montecristo and a new logo was designed for it: the yellow and red "crossed swords" logo the brand still bears today.

Through the efforts of Alfred Dunhill, Ltd., the Montecristo brand became incredibly popular worldwide and to this day accounts for roughly 50% of Habanos SA's worldwide cigar sales, making it the most popular Cuban cigar in the world. After the Cuban Revolution and the nationalization of the cigar industry in Cuba in 1961, Menéndez and García fled to the Canary Islands where they re-established the brand, but were later forced to quit due to copyright disputes with Cubatabaco. In the mid-1970's, the operation was moved to La Romana in the Dominican Republic and released for the US market, where Cuba's rights to the brand weren't recognized due to the embargo. Menéndez, García, y Cía is now owned by Altadis SA, who controls its distribution and marketing in the United States.

The original line had only five numbered sizes, with a tubed cigar added during the 1940's, but otherwise remained unchanged until after nationalization. With Menendez and Garcia gone after 1959, one of the top grade torcedores, José Manuel Gonzalez, was promoted to floor manager and proceeded to breathe new life into the brand. In the 1970's and 1980's, five new sizes were added: the A, the Especial No. 1 and 2, the Joyita, and the Petit Tubo. Three other sizes, the Montecristo No. 6, No. 7, and B, were released but subsequently discontinued, though the B can occasionally be found in very small releases each year in Cuba.

Through the 1970's and 1980's, Montecristo continued to rise in popularity among cigar smokers and firmly entrenched itself as one of Cuba's top selling cigar lines. The Montecristo No. 4 is, itself, the most popular cigar in the world market.

In 2004, another new edition to the regular line was made with the Edmundo, a large robusto-sized cigar, named for the hero of Dumas' The Count of Monte Cristo, Edmond Dantès.

Montecristo is also regularly chosen to be featured in Habanos SA's annual Edición Limitada selection of cigars with a darker vintage wrapper and there are numerous limited edition releases of special Montecristo cigars for special occasions, anniversaries, the annual Habanos Festival, charities, etc.

Montecristo also produces three machine-made cigarillos: the Mini, the Club, and the Purito.