Their three children, Paul Augustus (1805–1864), William (1805–1878), and Michael (1807–1889) also became artists. His relationship with his wife however deteriorated gradually over the years, which is detailed in papers stored at the library of the Victoria and Albert Museum. His strong Catholic beliefs prevented any chance of a divorce but they separated. He accused her of "bad conduct" but shied from providing details. In a letter to him in 1827 she blamed him entirely for the collapse of their marriage, suggesting cruelty, pederastic activities and adultery were the reasons, writing that one of his pupils, Harriet Gouldsmith, had told her Malready "preferred her little finger" to his wife and children, and accusing him having "had taken a low boy to your bed, and turned one adrift at midnight, to seek one at the house of an unmarried man."