Clare was the centre of the extensive lands belonging to the Honor of Clare in the eastern counties. The courts of the honor, as well as of borough and manor, were held by the lord's steward in the moothall at Clare. The lords were often in residence, and their great officials, steward, marshal, constable and others were normally at the castle. As a result the town was easily overawed, and it had little chance of free development. The Honor of Clare had become a Crown possession at the end of the fifteenth century and after 1558 it was included in the administration of the Duchy of Lancaster, as it is today. In Clare itself town government was in the hands of the headboroughs (known in medieval times as chief pledges), who met regularly at first four times a yeare and later in a twice-yearly court which was in effect the continuation of the medieval court leet. Moreover, the men who were elected headboroughs seem also to have been the most influential members of the church vestry, which at that time had a vast amount of civil as well as ecclesiastical work. Clare never developed fully as a borough.
This can best be seen in the way they obtained the demesne lands of the manor as a town pasture, a part of which is still called "the common". In the later Middle Ages there had been several changes in the manorial economy. Manors in the neighbourhood had suffered severely from the Black Death and other pestilences. For this and other reasons labour had become more scarce, wages rose, and the lords tried a number of expedients meant to be only temporary, but some of which proved permanent. At Clare parts of the manor were leased out, at first for short periods. Similarly the mills were farmed out. Then in 1495 the site of the whole manor was leased to Robert Turnebull. In 1554 Ambrose Gilbert, William Fryer and John Fenne representing the town paid on e hundred marks for a confirmation of this grant. The pasture was to be used for the benefit of those owning less that fifteen acres of land; according to the church records the common was divided into cattle walks, each tenant paying twenty pence for a summer, and eight pence for a winter walk. After the yearly rend of £3 6s. 8d. had been paid to the crown the poor in Clare were to be given any profits arising from the administration of the pasture.
Our knowledge of Clare in the early modern period is largely derived from the court rolls known as the Verdicts of the Headboroughs. In the courts, officials were elected as in medieval times, every yeare two constables, two aletasters or clerks of the market, every two years two bailiffs who were the senior headboroughs. Much of the town business was transacted in the church vestry, meeting once or more in the year, sometimes in the market house, sometimes at one of the inns, and elsewhere. The vestry controlled the administration of the common lands, electing two wardens to be in charge, also a bailiff or pinder of the pasture whose duty it was to impound stray cattle, keep up the fences and spread out dung and molehills. In the vestry the accounts of the churchwardens, overseers, surveyors and constables were supervised. The local administration of the poor law was in the hands of churchwardens and overseers, under the supervision of the justices of the peace. Pauper children were apprenticed out to masters in the neighbourhood. We do not know the date of the building of a House of Correction at Clare, but 1660 it was said to be badly in need of repair, and it was ordered in Quarter Sessions that a new House should be built. In the House the inmates were mainly occupied in the spinning of yarn and waving into cloth.