The relationship between medieval inquisitors and their orders was multilayered and sometimes tense. Inquisitors occupied an independent office, in whose affairs their superiors were forbidden to interfere, but they were not detached from their order. Many had already been senior officers in its hierarchy, and at the end of their term of office (itself determined by the order), they expected to return to similar posts. The provincial ministers and priors who appointed them were their colleagues. They were based in local convents, and relied on the order to supply the vicars, socii and much other assistance without which they could not function effectively. Despite their wide powers and freedoms in office, inquisitors also remained friars subject to their order's rules and discipline. The combination of independence in office and obedience outside it was both awkward for individuals to reconcile at a personal level, and hard to square with the needs of the job.

The Franciscan and Dominican orders agonised in different ways over their role in inquisition and the extent of control exercised over how their inquisitors did their jobs. Both were committed to opposing heresy, but they often struggled to strike an effective balance between the growing demands of the inquisitorial cuckoo and their wider mission. Tensions played out at many levels, among them demands on space in convents, calls on the time and help of brother friars, concern over the handling of money flowing in from confiscations and penalties and fear at the impact of heavy-handed inquisition decisions on the mendicants’ relationships with the local community. In the last quarter of the thirteenth century, a belated regulatory attempt was made to impose accounting control over inquisitors’ spending and require them to submit accounts at provincial chapters, something which had long been standard for offices of the order itself. These measures interacted rather uneasily with the parallel and intermittent demands of the papal Camera, which began in the 1290s. Inquisitorial excesses were formally condemned, but the seriousness of the orders’ control effort must be doubted because of the many examples where the orders’ hierarchies ignored or were complicit in financial misbehaviour. At the same time, the orders themselves developed a heavy reliance on financial input from inquisitors. Inquisition contributions supported building projects, the routine costs of provincial chapters and the lifestyle of senior office-holders. Such entanglements unavoidably compromised the orders’ role in standard-setting.