 Following the Restoration his remains were disinterred in 1661 and eventually placed in an elaborate tomb in St. Giles.The diarist John Nicoll recorded the event,

[A guard of honour of four captains with their companies] went out thaireftir to the Burrow mure quhair his corps wer bureyit, and quhair sundry nobles and gentrie his friendis and favorites, both hors and fute wer thair attending; and thair, in presence of sundry nobles, earls, lordis, barones and otheris convenit for the tyme, his graif [grave] was raisit, his body and bones taken out and wrappit up in curious clothes and put in a coffin, quhilk, under a canopy of rich velwet, wer careyit from the Burrow-mure to the Toun of Edinburgh; the nobles barones and gentrie on hors, the Toun of Edinburgh and many thousandis besyde, convoyit these corpis all along, the callouris [colours] fleying, drums towking [beating], trumpettis sounding, muskets cracking and cannones from the Castell roring; all of thame walking on till thai come to the Tolbuith of Edinburgh, frae the quhilke his heid wes very honorablie and with all dew respectis taken doun and put within the coffin under the cannopie with great acclamation and joy; all this tyme the trumpettis, the drumes, cannouns, gunes, the displayit cullouris geving honor to these deid corps.From thence all of thame, both hors and fute, convoyit these deid corps to the Abay Kirk of Halyrudhous quhair he is left inclosit in ane yll [aisle] till forder ordour be by his Majestie and Estaites of Parliament for the solempnitie of his Buriall.