In Protestant usage, a consistory designates certain ruling bodies in various churches. The meaning and the scope of functions varies strongly, also along the separating lines of the Protestant denominations and church bodies.

Starting in 1539 the term was used for a body taking over the jurisdiction in marital matters, and later also church discipline, so that Protestant consistories can be regarded as successors not to the papal consistory in Rome but rather to the courts of Roman Catholic bishops. In the Lutheran or Reformed states of imperial immediacy in the Holy Roman Empire episcopal offices were not staffed any more and the secular government assumed the function of the bishop (summepiscopate, summus episcopus), looked after by the consistories.

Not all Protestant churches adopted consistories, especially not collegially governed churches, often of Reformed or Presbyterian confession. Consistories were either bodies of local churches (mostly in the Reformed tradition), or parastatal entities, like in the French model, or they were governing bodies as part of the administration of Protestant state churches (Lutheran, Reformed and United Protestant alike). The rather governmental character of the consistory is the reason why the term was given up in many church bodies after the separation of religion and state and the concomitant abolition of the status as state church and the assumption of church independence.

In countries under French influence the Protestants, Calvinists and Lutherans alike (and the Jews as well, see Israelite consistories), made use of the term in the beginning of the nineteenth century with the enactment of the Organic Articles, when the movement for political emancipation demanded the creation of a representative body, whereas Napoleon's government simultaneously aimed at gaining influence onto the non-Catholic religious bodies. Roman Catholicism in Napoleon's realm was subject to the Concordat of 1801. The consistories in the French Empire could transact official business with a government in the name of the Protestants and vice versa. Furthermore, the desire for reform among the educated classes demanded the creation of a body vested with authority to render religious decisions.

"In Anglican churches the consistory is the diocesan court, usually presided over by the bishop's chancellor or commissary. It deals with a variety of issues at the diocesan level, and its decisions may be appealed to higher courts in the national church."

In the Lutheran tradition, and derived from that similarly in some united and uniting Protestant churches, the consistory is a body governing the ecclesiastical affairs in a specific ambit, comprising either all congregations (aka parishes) within a Protestant church body (thus forming a leading body, with executive and /or spiritual competence for a church), or only those in a district organisation (consistorial district; German: Konsistorialbezirk) or in a regional organisation (such as an ecclesiastical province; German: Kirchenprovinz). In the latter two cases, typical in churches with a congregational polity, the term consistory is also used to designate the geographical area administered by the consistory.

In 1539 Martin Luther and his associates established the Wittenberg Consistory [de] (1539–1816) in Wittenberg upon Elbe competent for the Lutheran church in the Saxon Electoral District [de] within the then realm of the Ernestine line of the House of Wettin. Although originally an ecclesiastical court of the Saxon Lutheran church, the consistory developed into an administrative body appointed by the sovereign to supervise the church within his state. In other Lutheran states the consistories took similar developments.

Consistories, forming executive body of a state church, had often great powers through the authority of the secular government. In history, before separating executive and juridical competences, consistories of Lutheran state churches with central executive powers, therefore usually consisting of jurisprudents and clergy, did also function as courts appointed to regulate ecclesiastical affairs. At times the consistories were parastatal offices in charge of all (Protestant) denominations (e.g. in Bremen-Verden) or even all religions (e.g. in Prussia, see Evangelical Church in Prussia from 1808 to 1816) in the respective territory. While Lutheran churches often still did not form legal entities distinct from the state, the consistories turned out to be the oldest body of many modern regional Protestant church bodies, which developed into independent legal entities in the 18th and 19th centuries.