In 1603 they jointly appealed with success to Philippe de Mornay against a decision of the synod of Gap on a polemical question.
Johnston had been offered the position of second minister in Haddington, East Lothian, but he retained his university chair till his death in October 1611.
In 1602 Johnston published at Amsterdam Inscriptiones Historicæ Regum Scotorum, continuata annorum serie a Fergusio I. ad Jacobum VI.
; præfixus est Gathelus, sive de gentis origine Fragmentum Andreæ Melvini; additæ sunt icones omnium regum nobilis Familiæ Stuartorum.
The Inscriptiones are a series of epigrammatic addresses to the Scottish kings from Fergus I to James VI; to the latter the work is dedicated.