Early stage works
Although Messager called some of his early stage works opéras comiques they have, Gervase Hughes suggests, more in common with opérette than their composer acknowledged. Nevertheless, Messager introduced adventurous modern harmonic details in his early pieces, and strove to raise the artistic standards of opérette to that of opéra comique while retaining the essential panache of the genre. Hughes finds the first stage works uneven in quality but La Fauvette du temple (1884) to contain two fine expressive duets as well as waltzes and polkas with "an Offenbach lilt". Hughes judges the next two scores, La Béarnaise and La Fauvette (both 1885), less satisfying but nonetheless at least as good as anything by Messager's older contemporaries Planquette, Serpette and Lecocq.

Wagstaff writes that the composer's most enduring work is the ballet score Les Deux Pigeons (1886) The piece is based on the fable The Two Pigeons by Jean de La Fontaine. The music is best known in the five-movement suite arranged from the full score, which includes the "Entrée de tziganes". Messager revived the ballet in 1906 in London and in 1912 in Paris in a shortened, two-act version. In 1961 John Lanchbery revised this for Frederick Ashton's new version of the ballet, with a closing reconciliation scene from earlier music and a passage transcribed from Véronique. This was first given at Covent Garden, is revived regularly by the Royal Ballet and has been staged by such other companies as CAPAB and Australian Ballet.

Isoline (1888), a musical fairy story ("conte des fées"), is neither an opérette nor an opéra comique. Writing in 1908, Fauré called it "one of the most poetic, most expressive works that have been written in France in the last twenty years",[133] but it made little impact. The score remained in obscurity until 1930 when Reynaldo Hahn staged the ballet section of the work at Cannes. The whole piece was revived at the Opéra-Comique in 1958; it failed again, but the ballet, unencumbered by the portentousness of the libretto, which weighs down the rest of the piece, has remained in the repertory.
1890s stage works​
The decade began well for Messager with the artistic and commercial success of La Basoche (1890). Février in his André Messager: Mon Maître, Mon Ami calls it "the last of the great nineteenth-century French comic operas" ("le dernier des grands opéras-comique français du XIX siècle")[136] and considers it of the greatest importance not only in Messager's career but in the history of French musical theatre. Hughes says it has a good claim to be the composer's masterpiece. The musicologist James Harding rates it "the best Messager had written to date ... one of his finest works".[118] When the work was given in London, a year after its Parisian premiere, the reviewer in The Times called it, "A work of great beauty and charm", although "the influence of Die Meistersinger is felt to an extent that is almost absurd both in the bright overture and again in the procession of the guild, but elsewhere the music is as original as it is charming".

With Madame Chrysanthème (1893), a four-act "lyric comedy" with no spoken dialogue, Messager reached a turning point in his development. The crux of the plot was the same as that later used by Puccini for Madama Butterfly (1904): a young Japanese geisha wooed and then abandoned by a foreign sailor. Messager's treatment of the story was praised for its sensitivity – reviewers in the Parisian press applauded him for raising opérette to the level of "comédie lyrique – but he was a self-critical artist, and he felt he had strayed too far in the direction of opera and away from his chosen genre. Harding suggests that the unusual seriousness of the score may be connected with the recent illness and death of Edith Messager. Both Hughes and Harding comment that Messager's score is subtler than Puccini's, but add that the almost total eclipse of Madame Chrysanthème by Madama Butterfly may be partly due to the relative effectiveness of their libretti. After this, Messager consciously simplified his style, greatly reducing the harmonic subtleties that had been characteristic of his earlier works.

The works from the middle of the decade were unsuccessful financially and artistically. Le Chevalier d'Harmental (1896), classed by Hughes as Messager's first true opéra comique ("in a somewhat pretentious style") was a failure, and an unpretentious opérette in the same year, La Fiancée en loterie, fared no better. After these disappointments Messager finished the 1890s with two considerable successes. Traubner describes Les P'tites Michu (1897) as "a sensational hit", and Harding calls it the best of Messager's opérettes so far (classing Le Basoche as opéra comique, as did its composer). The plot was not strikingly original: critics commented that its story of babies switched at birth was already very familiar from Gilbert and Sullivan operas.  Traubner describes the piece as "one of those unusual works that begin well enough and gets better and better". Setting a scene in the market of Les Halles was not innovative, but Messager's chorus for the marchands and marchandes was out of the ordinary, and Traubner also singles out the duet for the Michus in Act 1: "clever, lilting ... pulsating with an elegance and grace that other operetta composers have failed to obtain". He also judges the finales as outstanding, including a waltz number that in other hands would be predictable but is turned by Messager into something much more symphonic.

The final work from the decade was Véronique. Messager described it as an opéra comique, but commentators have classed it as a mixture of opérette and opéra comique.The score contains two of the composer's best known numbers, the "Swing duet" ("Poussez, poussez l'escarpolette") and the "Donkey duet" ("De ci, de la"). When the work was revived at the Proms in London in the 1960s, the music critic of The Times commented, "Charming as it can prove in the theatre, the music alone is a little thin, with none of the piquancy that – thanks perhaps to Gilbert – redeems Messager's famous English contemporary Sullivan ... but Véronique has plenty of pretty things". It became and has remained the composer's most performed musical theatre piece.

20th century
Marion Green and Maggie Teyte in Monsieur Beaucaire, 1919
Messager's work running opera houses in Paris and London limited his composing between Véronique and the period after the First World War. Fortunio (1907) was a rare example in his oeuvre of a sung-through opera. Eight decades later the critic Edward Greenfield described it as "a long-buried jewel of a piece ... an improbable cross between musical comedy and Tristan und Isolde". From 1919 onwards Messager composed no more opéras comiques. Among his post-war stage works, Monsieur Beaucaire, a "romantic operetta" (1919), was his second work to an English libretto. French critics were inclined to look down on "Messager's English operetta" as over-sweet and sentimental to suit Anglo-Saxon tastes. Harding comments that the composer was successful in his attempt to produce an English flavour: one number is "pure Edward German" and there is much pastiche throughout the score. Despite the critics the piece ran well not only in Britain and the US, but also in France, with more than 300 performances in Paris and a long life in French provincial theatres.

Of Messager's 1920s comédies musicales the best known is L'Amour masqué (1923). The Théâtre Édouard VII where it was premiered had a small orchestra pit, and Messager developed a new style of orchestration to deliver his desired musical effects with a small number of players. Harding comments that the piece was up-to-date enough to include a tango, "a beautifully written example with luscious harmonies that by contrast show up the threadbare nature of most other efforts of the time".