At his father's death in 1542, Thomas inherited Allington Castle and Boxley Abbey in Kent, but found both estates encumbered by debt. Further financial difficulties arose from the fact that, having been unfaithful to his wife (rumour had it that they were both unfaithful), the elder Wyatt separated from her. He had a child named Francis Wyatt, whose mother was Elizabeth Darrell, an unmarried daughter of Sir Edward Darrell of Littlecote House in Wiltshire. The elder Sir Thomas left Elizabeth property in Dorset, thus diminishing his son's inheritance. Nonetheless, the younger Thomas was evidently on friendly terms with his half-brother Francis, to whom he made a gift of his manor of Tarrant.