The Church in Nazi Germany was subjected to as much pressure as any other organisation in Germany. Any perceived threat to Hitler could not be tolerated - and the churches of Germany potentially presented the Nazis with numerous threats.
In 1933, the Catholic Church had viewed the Nazis as a barrier to the spread of communism from Russia. In this year, Hitler and the Catholic Church signed an agreement that he would not interfere with the Catholic Church while the Church would not comment on politics. However, this only lasted until 1937, when Hitler started a concerted attack on the Catholic Church arresting priests etc. In 1937, the pope, Pius XI, issued his "Mit brennender Sorge" statement ("With burning anxiety") over what was going on in Germany. However, there was never a total clampdown on the Catholic Church in Germany. It was a world-wide movement with much international support.
The Protestant Church was really a collection of a number of churches - hence they were easier to deal with. The Protestants themselves were split. The "German Christians" were lead by Ludwig Muller who believed that any member of the church who had Jewish ancestry should be sacked from the church. Muller supported Hitler and in 1933 he was given the title of "Reich Bishop".
Those who opposed the views of Muller were called the "Confessing Church". This was led by Martin Niemoller. He was famous in Germany as he had been a World War One U-boat captain. Therefore, he was potentially an embarrassing foe to the Nazis. Regardless of this, he was not safe from the Gestapo who arrested him for opposing Hitler. Niemoller was sent to a concentration camp for 7 years where he was kept in solitary confinement. Many other Confessional Church members suffered the same fate.
In 1936, the Reich Church was created. This did not have the Christian cross as its symbol but the swastika. The Bible was replaced by "Mein Kampf" which was placed on the altar. By it was a sword. Only invited Nazis were allowed to give sermons in a Reich Church.
In 1941, a secret report compiled by Protestants stated that children in Germany were being brought up minus a Christian education. It stated that the Nazis confiscated vast areas of church property and that the Catholic Church in Germany was suffering from the same fate.