The early years of Henry VIII's reign was an incipient period for English ciphers. See another article for the earliest English ciphers.
See another article.
A letter from Dr. Magnus (Wikipedia) to Wolsey, Edinburgh, 19 April 1525 (Cotton MS Caligula B VII BL, f.62-66) includes a paragraph in cipher. An incomplete (and partially incorrect) key is attached, and allows reconstruction of the cipher as below. The note in the margin turned out to be an excerpt of the plaintext.
Add MS 25114 (BL) includes a letter in cipher from Thomas Cromwell to Gardiner from 26 February 1536, appended to a letter in clear dated 25 February (f.249-252). The plaintext is printed in Roger Bigelow Merriman (1902), Life and Letters of Thomas Cromwell, vol. II, p.5 (Internet Archive, Google) (There is a note of a nineteenth-century(?) archivist on f.250v, dating this letter to 1537.).
The cipher can be reconstructed as follows.
Merriman (1902) prints three letters in cipher from Thomas Cromwell to Sir Thomas Wyatt, who was sent to the court of the Emperor in 1536 (Wikipedia). The originals are in Harley MS 282.
p.113 [no.238] Cromwell to Sir Thomas Wyatt, 11 February 1538 (Harley MSS 282 ff.167, 159) (This letter uses many nulls at the beginning.)
p.122 [no.244] Cromwell to Sir Thomas Wyatt, 1 March 1538 (Harley MSS 282 ff.175-182)
p.140 [no.261] Cromwell to Sir Thomas Wyatt, 10 May 1538 (Harley MSS 282, ff.191, 202)
The cipher can be reconstructed as follows.
According to Garett Mattingly, Renaissance Diplomacy, p.215 (Internet Archive), and Arthurson, "Espionage and Intelligence from the Wars of the Roses to the Reformation", p.150, experts under Thomas Cromwell broke the cipher of the Imperial ambassador, Eustache Chapuys by 1535. I have not been able to identify their sources.
Add MS 32650 (BL) includes a letter mostly in cipher from Sir Ralph Sadler, ambassador to Scotland, to Henry VIII, Edinburgh, 22 April [1543] (ff.214-219).
Add MS 32652 (BL) and Add MS 32653 (BL) include many letters (1543) from Sadler to Henry VIII, Charles Brandon, Duke of Suffolk, Cuthbert Tunstall, Bishop of Durham, or the Privy Council.
Sadler's letters are printed in Arthur Clifford (ed.) (1809), The State Papers and Letters of Sir Ralph Sadler, vol.I (Google), vol.II (Google).
The cipher used in these letters can be reconstructed as follows.
Add MS 32657 (BL), ff. 4r-6v, includes a letter from Sir James Wylford, Governor of Haddington, to William Grey, 13th Baron Grey of Wilton and Lord Lieutenant of the North, dated Haddington, 2 July [1548].
The cipher can be reconstructed as follows.
See another article.
S. Tomokiyo, "Earliest English Diplomatic Ciphers"
S. Tomokiyo, "Ciphers during the Reign of Queen Elizabeth I"