He wrote a work against the followers of Eutyches and Dioscorus, entitled , It was divided into twelve parts, and was undertaken at the suggestion of a certain prelate, one Julianus, in reply to an anonymous Eutychian writer, who had published a book deceitfully entitled , and whom Photius supposed to be Basilius, a presbyter of Cilicia. This Basilius wrote a reply to Joannes in very abusive style, charging him, among other things, with being a Manichaean, and with restricting Lent to a period of three weeks, and not abstaining from flesh even in that shortened period.

Certain Παραθέσεις, to the works of the pseudo Dionysius Areopagita, which Usher has observed to be mingled in the printed editions of Dionysius with the of St. Maximus, have been ascribed to Joannes of Scythopolis. Anastasius Bibliothecarius in the eighth century made a Latin translation of these mingled scholia, not now extant, in which he professed to distinguish those of Maximus from those of Joannes by the mark of a cross. Fabricius identifies the of Joannes with the cited by Joannes Cyparissiota as by Dionysius of Alexandria.