After the Japanese occupied the Indies in early 1942, on 9 March 1942 Governor-General Tjarda van Starkenborgh Stachouwer and head of the Royal Netherlands East Indies Army General Hein ter Poorten capitulated.
This brought numerous changes in the governance of the archipelago, reducing the quality of life for non-Japanese.
In his diary, Soegijapranata wrote of the invasion that "fires were everywhere ... no soldiers, no police, no workers.
The streets are full of burnt out vehicles.
 ... Luckily least there are still some lawmakers and Catholics out there.
They work as representatives of their groups to ensure the city is in order."

The occupation government captured numerous (mostly Dutch) men and women, both clergy and laymen, and instituted policies that changed how services were held.
They forbade the use of Dutch in services and in writing, and seized several church properties.
Soegijapranata attempted to resist these seizures, at times filling the locations with people to make them unmanageable or indicating that other buildings, such as cinemas, would serve Japanese needs better.
When the Japanese attempted to seize Randusari Cathedral, Soegijapranata replied that they could take it only after decapitating him; the Japanese later found another location for their office.
He prevented the Japanese from taking Gedangan Presbytery, where he lived, and assigned guardians for schools and other facilities to prevent seizure.
These efforts were not always successful, however, and several Church-run institutions were seized, as were church funds.

Soegijapranata was unable to prevent Japanese torture of prisoners of war, including the clergy, but was himself well-treated by the Japanese forces; he was often invited to Japanese ceremonies, but never attended, sending bouquets in his stead.
He used this position of respect to lobby for fair treatment of those interned.
He successfully petitioned the Japanese overlords to exempt nuns from the paramilitary draft and allow them to work at hospitals.
He and the Catholic populace also gathered food and other supplies for interned clergy, and Soegijapranata kept in contact with the prisoners, supplying and receiving news, such as recent deaths, and other information.

As the number of clergy was severely limited, Soegijapranata roamed from church to church to attend to parishioners, actively preaching and serving as the de facto head of the Catholic Church in the country; this was in part to counteract rumours of his detention by the Japanese.
He travelled by foot, bicycle, and carriage, as his car had been seized.
He sent pastors to apostolic prefectures in Bandung, Surabaya, and Malang to deal with the lack of clergy there.
Soegijapranata worked to ensure that the seminary would continue to produce new pastors and appointed the recently ordained Father Hardjawasita as its rector.
He also granted native priests the authority to perform marriages.
To calm the Catholic populace, he visited their homes and convinced them that the streets were safe.
After the Japanese occupied the Indies in early 1942, on 9 March 1942 Governor-General Tjarda van Starkenborgh Stachouwer and head of the Royal Netherlands East Indies Army General Hein ter Poorten capitulated. This brought numerous changes in the governance of the archipelago, reducing the quality of life for non-Japanese. In his diary, Soegijapranata wrote of the invasion that "fires were everywhere ... no soldiers, no police, no workers. The streets are full of burnt out vehicles. ... Luckily least there are still some lawmakers and Catholics out there. They work as representatives of their groups to ensure the city is in order."
The occupation government captured numerous (mostly Dutch) men and women, both clergy and laymen, and instituted policies that changed how services were held. They forbade the use of Dutch in services and in writing, and seized several church properties. Soegijapranata attempted to resist these seizures, at times filling the locations with people to make them unmanageable or indicating that other buildings, such as cinemas, would serve Japanese needs better. When the Japanese attempted to seize Randusari Cathedral, Soegijapranata replied that they could take it only after decapitating him; the Japanese later found another location for their office. He prevented the Japanese from taking Gedangan Presbytery, where he lived, and assigned guardians for schools and other facilities to prevent seizure. These efforts were not always successful, however, and several Church-run institutions were seized, as were church funds.
Soegijapranata was unable to prevent Japanese torture of prisoners of war, including the clergy, but was himself well-treated by the Japanese forces; he was often invited to Japanese ceremonies, but never attended, sending bouquets in his stead. He used this position of respect to lobby for fair treatment of those interned. He successfully petitioned the Japanese overlords to exempt nuns from the paramilitary draft and allow them to work at hospitals. He and the Catholic populace also gathered food and other supplies for interned clergy, and Soegijapranata kept in contact with the prisoners, supplying and receiving news, such as recent deaths, and other information.
As the number of clergy was severely limited, Soegijapranata roamed from church to church to attend to parishioners, actively preaching and serving as the de facto head of the Catholic Church in the country; this was in part to counteract rumours of his detention by the Japanese. He travelled by foot, bicycle, and carriage, as his car had been seized. He sent pastors to apostolic prefectures in Bandung, Surabaya, and Malang to deal with the lack of clergy there. Soegijapranata worked to ensure that the seminary would continue to produce new pastors and appointed the recently ordained Father Hardjawasita as its rector. He also granted native priests the authority to perform marriages. To calm the Catholic populace, he visited their homes and convinced them that the streets were safe.
Albertus Soegijapranata