Among Aubigné's prose works, the Confession catholique du sieur de Sancy, first published in 1660, is a parody, ironically dedicated to Cardinal Duperron, of the tortuous explanations offered by Protestants who followed Henry IV's example of abjuration. His comment on life and manners ranges more widely in the Adventures du baron de Faeneste (1617), in which the Gascon Faeneste represents attachment to outward appearances (le paraître) while honest squire Énay, embodying the principle of true being (l'être), tries to clear Faeneste's mind of cant. The Histoire universelle deals with the period from 1553 to 1602, with an appendix to cover the death of Henry IV (1610); an unfinished supplement was meant to bring the story up to 1622. The chief interest of the Histoire lies in its eyewitness accounts and in the liveliness of Aubigné's writing.

His major poem in seven cantos, the Tragiques, begun in 1577 (published 1616), celebrates the justice of God, who on the Day of Doom will gloriously avenge his slaughtered saints. The subject matter, the sectarian bias, and the uneven composition and expression are offset by many passages of great poetic power, often lyrical in their Biblical language and noble in the despairing intensity of their invective. The scope of the design confers epic grandeur on the work. Modern research on Baroque literature has awakened interest in Aubigné's youthful love poetry, collected in the Printemps (1570–73, unpublished). It remained in manuscript until 1874. In these poems the stock characters and phraseology, modelled on Petrarch, are transmuted into a highly personal style, full of tragic resonances, by Aubigné's characteristic vehemence of passion and force of imagination.