The Cotton family, who hailed from Coton (q.v.) and later went on to acquire the Bellaport Hall estate (q.v.), were the owners of Alkington from the late fourteenth century. They came into the property in 1398 through the marriage of Roger Cotton with Ellen, the daughter and heiress of John Gremyton of Alkington.

Seemingly from 1572, the Cottons began building a timber-framed house at Alkington, which survives as the south-west corner of the present house and was later rebuilt in brick. To this earlier section was added an L-plan range in 1592, of two storeys with attics. The two elements of the house combined make up a double-pile plan which, along with Acton Scott and Whitehall, was one of the earliest in the county. In spite of alteration – namely the nineteenth-century, single-storey, gabled north porch – the house remains a striking sight. Its north and east fronts are a fanfare of diapered brickwork that is set off by stonework plinth, quoins, coping, ball finials and mullioned and transomed windows. On the east side, the twin gables of the front are divided by a projecting chimney-stack that is crowned by a pair of diagonally set square chimney-shafts. A further similar stack stands around the corner, to the south, at the point where a tower projects from the side of the house with a crow-stepped gable which recalls those of Bellaport Old Hall.

The brick build is thought to have been commissioned by William Cotton (d. 1608), perhaps funded in part by his younger brother Sir Allen Cotton Kt, a draper, Sheriff of London (1616–17) and Lord Mayor of London (1625–6). William Cotton’s son, Sir Rowland Cotton (b. circa 1577) – the nephew of Sir Allen – owned Alkington by 1619.