Felicitas ultimi saeculi (Londinium : Hodkinson, 1640)

A forme of wholsome words, or, An introduction to the body of divinity in three sermons on 2 Timothy, I.13 (London : J.R. for J. Bellamy, H. Overton, A. Crook, J. Rothwell, R. Sergeir, I. Crook, D. Frere, and Ralph Smith, 1640)

The heauenly conuersation and the naturall mans condition In two treatises. By Iohn Stoughton, Doctor in Divinitie, sometimes fellow of Emanuel Colledge in Cambridge; and late preacher of Gods word in Alderman-bury London (London : T. C[otes] for John Bellamie, and Ralph Smith, and are to be sold at the three Golden Lyons, 1640)

Seaven sermons, preached upon severall occasions .. (London : J.D. for John Bellamie [etc.], 1640)

XI. choice sermons preached upon selected occasions, in Cambridge. Viz. I. The preachers dignity, and duty: in five sermons, upon 2. Corinth. 5. 20. II. Christ crucified, the tree of life: in six sermons, on 1. Corinth. 2. 2. By John Stoughton, Doctor in Divinity, sometimes fellow of Immanuel Colledge in Cambridge, late preacher of Aldermanburie, London. According to the originall copie, which was left perfected by the authour before his death. (London : R. B[adger] for Iohn Bellamie, Henry Overton, Iohn Rothwell, and Ralph Smith, 1640)