The second marriage of Sir Thomas Hoo belonged to the period of his service in Hastings and Normandy, when he became titled. He married Eleanor Welles (one of the four daughters of Lionel de Welles, 6th Baron Welles and Joan Waterton, daughter and heiress of Robert Waterton (c. 1360–1425)), and they had three daughters, Anne, Eleanor and Elizabeth. These daughters were born between 1447 and 1451, as their ages are given in their father's "inquisition post mortem". In November 1445 Leo Welles made a covenant with Sir Thomas and Eleanor, by which Thomas acknowledged Welles's right of gift, and Welles granted to them, and to their male heirs forever, the manors of Hoo, Mulbarton, Offley and Cokernho, and the advowsons of Mulbarton and Offley, with remainders (successively) to the male heirs of the body of Sir Thomas, or to Thomas Hoo his brother and to the male heirs of his body, or to the heirs of the body of Sir Thomas, or to the heirs of the body of Thomas Hoo, or (failing all these) finally to the right heirs of Sir Thomas. The lands brought by Sir Thomas to the marriage were thereby secured to the Hoo descent through either brother. In 1447 Welles also remarried, to Margaret Beauchamp of Bletso.