In 1795, Paul Anton Esterházy's successor, Nikolaus II, decided to reform the Esterházy orchestra. In the process, he invited Haydn back to serve as active Kapellmeister—rejuvenating the purely nominal post the composer had held for the previous five years. Compared to his previous 30 years of service to the family, Haydn's new duties were still minimal, but they included the annual composition of a mass to celebrate the name day of Princess Josepha Maria in Eisenstadt, forty kilometers south of Vienna.

On the first page of his autograph manuscript of the C major mass, Haydn wrote, "Missa in tempore belli" (Mass in time of war). At the time, Austria was engulfed in a war with the French, and Napoleon was advancing from victory to victory unchecked. In August 1796, precisely when Haydn was at work on the C major mass, the Austrian government issued an order for general mobilization. Some writers have suggested that the baleful timpani part in the Agnus Dei reflects Haydn's reaction to the escalating military conflict; these timpani passages inspired the work's nickname, "Paukenmesse" (Timpani Mass).

Scholars are unsure of the date and place of the first performance. It may have taken place on September 13, 1796 in Eisenstadt, but there is some evidence that this was another mass, the Missa St. Bernardi. Some suggest it was first performed on September 29, 1797, in Eisenstadt. However, because the "Missa in tempore belli" formed part of a service in Vienna on the feast of St. Stephen (December 26) in 1796, it is more likely that the work was finished and given its premiere in 1796.

The Mass in C major is scored for soprano, alto, tenor, and bass soloists, a four-voice mixed choir and a large orchestra with paired woodwinds, trumpets and continuo (organ). Different recordings may feature varied instrumentation during some parts of the mass, as there exist two versions.

The symphonic character of the mass is evident from the opening of the Kyrie with its pulsating accompaniment in the strings and the imitations between the voices and woodwinds. After the slow introduction for chorus and orchestra closes on the dominant the soloists take over at an Allegro tempo. The climax of the movement occurs near the end, when the chorus loudly intones the only setting of Christe eleison in the whole movement on a sustained dominant seventh chord.

The divisions in the Gloria and Credo are based more on the passages of text than on musical considerations. The most poignant section of the Gloria is the "Qui tollis," where the tempo shifts abruptly from Vivace to Adagio and the key from C major to D major. A solo cello introduces the section's main theme, which is then taken up by the bass soloist. The antiphonal pairing of chorus voice parts in the "Amen" of the Gloria is only one example of the numerous textures Haydn develops throughout this rich work. Haydn's shift back to C major at the Quoniam is also very abrupt.

Haydn separates the Benedictus from the Sanctus and sets it in the tonic minor until about the midpoint, where the mode shifts to major. After the first line of the Agnus Dei the timpani enter with the quiet, rapid-fire motive that inspired the mass' second sobriquet. The dark atmosphere of the opening measures gives way to a brighter C major. Possibly reflecting the piece's historical context, nearly three-quarters of the movement is devoted to setting three words, "dona nobis pacem" (grant us peace).

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