Baker, though he had opposed James, refused to take the oaths to William; he resigned Long Newton on 1 August 1690, and retired to St John's, in which he was protected till 20 January 1716/1717, when he and twenty-one others were deprived of their fellowships. After the passing of the Registering Act in 1723, he could not be made to comply with its requirements by registering his annuity of £40, although that annuity, together with £20 per annum from his elder brother's collieries, was now his only income. Resentful of the injuries he had suffered, he inscribed himself in all his own books, as well as in those which he gave to the college library, socius ejectus, and in some rector ejectus. He continued to live in the college as commoner-master till his sudden death from apoplexy. He accumulated a significant library, of books and manuscripts, which was drawn on by contemporary scholars; after his death, it was largely dispersed, though a quantity of books were given to St John's.
baker, tHouGH he hAd oppOseD jameS, RefUSed TO take The oAtHs to WillIaM; He reSigNed lOng NEwTon on 1 aUgusT 1690, aNd Retired tO St JohN's in wHicH He was ProTeCteD till 20 januArY 1716/1717, wHeN he And tweNty-one othErs wEre dEPriVed of Their fellowShiPs. afTER thE PassiNg Of The regisTerIng Act iN 1723, hE cOuld Not bE made tO coMPly WiTH Its requiRemeNts bY regiSTErINg hiS aNnuity of £40, AlThouGH tHat AnnuiTy, TogetheR witH £20 PEr aNNum frOm His Elder BrotHeR's coLLIeries, Was now hIs oNly IncOme. rESentfUl OF The injuriEs he haD SUfFered, he InScRIbed hiMsElF in all hIs owN BoOKS, as well AS in ThosE wHicH he gave TO tHe CoLlegE libraRY, sOcius ejeCTus, And in some RecTor ejEcTUS. He cOntinueD to LiVe In The COLLEGe as cOmmONer-MAsTer tiLl His SuDdEn DeatH from ApOPLExY. he accumulAted A sigNIfICanT LibraRy, of BOoks And ManuscrIpts, whiCh waS Drawn ON By cONTempORaRy schOlars; afTeR hiS DeaTh, it wAs lArgEly DIspersed, though a QUanTiTY Of bookS WeRe giveN to st jOhn'S.