Many of John Jones's transcripts of Welsh and other manuscripts were made by him whilst he was in prison. His first transcript (now Pen. MS. 361) was made in 1598, whilst he was at Shrewsbury. Thereafter he was very assiduous; over a hundred manuscript volumes in his hand, and most of them in the particular type of orthography which he adopted (for details of his orthography see the thesis mentioned above) have survived, mainly in the Hengwrt-Peniarth collection. It was his association with Robert Vaughan of Hengwrt (q.v.), the famous collector of manuscripts, and himself a notable copyist, which accounts for such a large number of John Jones's transcripts being preserved in the Hengwrt-Peniarth group; there are examples also in the Mostyn, Llanstephan, and Additional MSS. in the National Library, at Cardiff, and in the British Museum. Some idea of the different types of texts — verse, prose, vocabularies in various languages, etc. — which he copied (or compiled) can be obtained from a study of Dr. J. Gwenogvryn Evans's catalogues compiled for the Hist. MSS. Comm. What is important about John Jones's copying is that he was a calligrapher and not a mere transcriber: his initial capital letters, tail-pieces, etc., although not uniformly good, show that he aimed at something more than a faithful transcript of the original text — he wished that copy to be an artistic copy with the addition of embellishments by himself. All his work is in black upon white. Sometimes the initials are in open-work with the interstices filled in solid black, and, whereas many of his initial capitals are capable of reproduction, others can no longer be reproduced or represented because the ink which he used in some of his manuscripts had too high a sulphur content, the result being that the paper has been consumed by the ink. He probably took many of his models, particularly for his initial capitals and head-and-tail-pieces, from 16th cent. Italian works on penmanship (some, however, are undoubtedly of his own designing); in this connection it is interesting to compare his ‘Collection of Alphabets’ (Pen. MS. 307) with published Italian works on penmanship (particularly Libro di M. Giovan. Battista, 1545) which survive in the Hengwrt-Peniarth collection in the National Library. But whether these Italian works belonged to John Jones or to Robert Vaughan cannot be determined with any certainty, although one of them was certainly used by Jones. There are also traces of the influence of German penmen and, as might be expected, there was a Celtic influence.

Tradition speaks of an arrangement made between John Jones and Robert Vaughan whereby the survivor was to inherit the collection of the other: this belief is, however, difficult to accept, because Robert Vaughan, who had sons, would hardly have made such an arrangement. It has been suggested that John Jones’ transcripts came to Vaughan in repayment for loans made by the latter to the transcriber.

The exact date of John Jones's death has not been ascertained, but it is possible that he was alive in 1658. (Drafts of letters from Robert Vaughan to ‘Mrs. Jones of Kelliloveday’ and to her father, Peter Griffith, Caerwys, are in Pen. MS. 270.)