Protestantism, and Christianity in general, also encountered an intellectual onslaught from thinkers who declared that the advance of science and of history proved the Bible, and therefore Christianity, untrue. The great issue for Protestants and all Christians in the 19th century was the question of biblical criticism; i.e., whether a person could be a Christian and even a good Christian though he held some parts of the Bible to be untrue. On the one hand, Protestantism stood by the Bible and declared that the truth of God came from it. On the other, Protestantism rested in part on a fundamental belief in the liberty of the human spirit as it encountered the Bible. Protestantism was thus seldom friendly to the tactic of meeting argument merely by excommunication or by the blunt exercise of church authority. The theological faculties of German universities, where the question of biblical criticism was first raised, suffered much internal stress, but they arrived at last at the conviction that reasoned criticism—even when it produced conclusions opposed to traditional Christian thinking—should be met by refutation rather than by authority. Thus German Protestantism showed an open-mindedness in the face of new knowledge that was influential in the 19th century. Owing in part to this German example, the Protestant churches of the main tradition—Lutheran, Reformed, Anglican, Congregational, Methodist, and many Baptist communities—adjusted themselves relatively easily (from the intellectual point of view) to the advances of science, to the idea of evolution, and to progress in anthropology and comparative religion.

In such a flux of ideas, with the Protestant tradition seemingly under internal attack from liberal Protestants, there was naturally a wide variety of approaches, both in philosophy and history. The German philosopher G.W.F. Hegel (1770–1831) proposed that Christianity should be restated as a form of Idealistic philosophy. This view was influential both among German thinkers and Oxford philosophers of later Victorian England. This approach, however, was subjected to critique, the most powerful of which was published by the Danish philosopher Søren Kierkegaard, who argued that philosophy failed to account for the depths and tragedies of human existence. An earlier opinion sought to justify Christianity on the basis of the religious feelings commonly found in humanity. The influential German theologian F.D.E. Schleiermacher (1768–1834) attempted to infer the Christian and biblical system of thought from an examination of human religious experience. Throughout the 19th century the appeal to religious experience was fundamental to liberal Protestant thinking, especially in the attempt to meet the views of modern science. Probably the most important of the successors to Schleiermacher was Albrecht Ritschl (1822–89), who wholly rejected the ideas of Hegel and the philosophers. He distinguished himself sharply from Schleiermacher by repudiating general religious experience and by resting all his thought upon the special moral impact made by the New Testament on the Christian community. Between 1870 and 1918 the Ritschlian school was one of the leading theological schools of Protestant thought.

Meanwhile, scholars made great strides in the study and exposition of the Bible. Freed from the necessity of defending every one of its details as historical truth, university professors put the books of the Bible into a historical setting. German biblical scholars, many of whom were influenced by Hegel, were the first to use the new approach freely. Ferdinand Christian Baur (1792–1860) of the University of Tübingen applied the methods of Hegelian philosophy to the books of the New Testament, which he conceived to be products of the clash between the Jewish Christians led by Peter and the Gentile Christians led by Paul. This theory, known as the Tübingen theory, soon receded in influence; but Baur’s commentary on New Testament texts remained a landmark in the study of the Bible. A number of excellent biblical scholars appeared after Baur, including Joseph Barber Lightfoot (1828–89) of Cambridge who demolished the Tübingen theory by showing the later 1st-century origin of most of the New Testament texts. Adolf von Harnack (1851–1930) of Berlin vastly enlarged the understanding of early Christianity. Insisting that the simple message of Jesus had been obscured by church dogma, he defined the essence of Christianity as love of God and neighbour. Harnack’s work also summarized the results of a century that was revolutionary in the area of biblical study.