The site Earliest Known Uses of Some of the Words of Mathematics provides just that, going into great detail where necessary about the history of the words used for concepts:
SUBTRACT. When Fibonacci (1201) wishes to say “I subtract,” he uses some of the various words meaning “I take”: tollo, aufero, or accipio. Instead of saying “to subtract” he says “to extract.”
In English, Chaucer used abate around 1391 in Treatise on the Astrolabe: “Abate thanne thees degrees And minutes owt of 90″ (OED2).
In a manuscript written by Christian of Prag (c. 1400), the word “subtraction” is at first limited to cases in which there is no “borrowing.” Cases in which “borrowing” occurs he puts under the title cautela (caution), and gives this caption the same prominence as subtractio.
In Practica (1539) Cardano used detrahere (to draw or take from).
In 1542 in the Ground of Artes Robert Recorde used rebate: “Than do I rebate 6 out of 8, & there resteth 2.”
In 1551 in Pathway to Knowledge Recorde used abate: “Introd., And if you abate euen portions from things that are equal, those partes that remain shall be equall also” (OED2).
Digges (1572) writes “to subduce or substray any sume, is wittily to pull a lesse fro a bigger number.”
Schoner, in his notes on Ramus (1586 ed., p. 8), uses both subduco and tollo for “I subtract.”
In his arithmetic, Boethius uses subtrahere, but in geometry attributed to him he prefers subducere.
The first citation for subtract in the OED2 is in 1557 by Robert Recorde in The whetstone of witte: “Wherfore I subtract 16. out of 18.”
Hylles (1592) used “abate,” “subtact,” “deduct,” and “take away” (Smith vol. 2, pages 94-95).
From Smith (vol. 2, page 95):
The word “subtract” has itself had an interesting history. The Latin sub appears in French as sub, soub, sou, and sous, subtrahere becoming soustraire and subtractio becoming soustraction. Partly because of this French usage, and partly no doubt for euphony, as in the case of “abstract,” there crept into the Latin works of the Middle Ages, and particularly into the books printed in Paris early in the 16th century, the form substractio. From France the usage spread to Holland and England, and form each of these countries it came to America. Until the beginning of the 19th century “substract” was a common form in England and America, and among those brought up in somewhat illiterate surroundings it is still to be found. The incorrect form was never popular in Germany, probably because of the Teutonic exclusion of international terms.
Thanks to Grant Barrett for the link.