After the Dutch recognised Indonesia's independence on 27 December 1949, following a several month-long conference in the Hague, Soegijapranata returned to Semarang.
The post-revolution period was marked by a drastic increase in enrolment at the nation's seminary; the 100th native Indonesian clergyman was ordained in 1956.
The government, however, enacted several laws that limited the Church's ability to expand.
In 1953 the Ministry for Religion decreed that no foreign missionaries would be allowed into the country, and a subsequent law prohibited those already in Indonesia from teaching.
In response, Soegijapranata encouraged eligible clergy to apply for Indonesian citizenship, circumventing the new laws.

Aside from overseeing the new clergy, Soegijapranata continued to work towards Catholic education and prosperity, similar to his pre-war work.
He emphasised that students must not only be good Catholics, but also good Indonesians.
The Church began further development of its schools, ranging from elementary schools to universities.
Soegijapranata also began reforming the Church in his apostolic vicariate, making it more Indonesian.
He advocated the use of local languages and Indonesian during mass, allowing it throughout his diocese beginning in 1956.
In addition, he pressed for the use of gamelan music to accompany services, and agreed to the use of wayang shows to teach the Bible to children.

As the Cold War heated up, tensions developed between the Church in Indonesia and the Indonesian Communist Party (Partai Komunis Indonesia, or PKI).
Soegijapranata believed that the PKI was making progress with the poor through its promises of workers' rights in a communist-led union.
To combat this, he worked with other Catholics to establish labour groups, open to both Catholics and non-Catholics.
He hoped that these would empower workers and thus limit the PKI's influence.
One such labour group was Buruh Pancasila, which was formed on 19 June 1954; through the organisation Soegijapranata helped promote the state philosophy of Pancasila, literally "the five tenets".
The following year the Church Representatives Conference of Indonesia (Konferensi Waligereja Indonesia, or KWI), recognising Soegijapranata's devotion to the poor, put him in charge of establishing social-support programmes throughout the archipelago.
On 2 November 1955, he and several other bishops issued a decree denouncing communism, Marxism, and materialism, and asking the government to ensure fair and equitable treatment for all citizens.
Relations between Indonesia and the Netherlands continued to be poor, specifically in regard to control of West Papua, historically under Dutch control but claimed by Indonesia.
Soegijapranata firmly supported the Indonesian position; West Papua was annexed in 1963.

There was also friction within the Catholic groups, first over Sukarno's 1957 decree that he was president for life and establishment of a guided democracy policy.
A faction, led by Soegijapranata, supported this decree, while Catholic Party leader I. J. Kasimo's faction was heavily against it.
Sukarno, who had a good working relationship with Soegijapranata, asked the vicar to join the National Council, a request that Soegijapranata refused; he did, however, assign two delegates to the Council, ensuring Catholic representation.
This, along with Soegijapranata's support of Sukarno's decree on 5 July 1949 calling for a return to the 1945 constitution, resulted in Bishop of Jakarta Adrianus Djajasepoetra's denunciation of Soegijapranata as a sycophant.
However, Soegijapranata was strongly against Sukarno's idea of Nasakom, which based part of the nation's government on communism.
After the Dutch recognised Indonesia's independence on 27 December 1949, following a several month-long conference in the Hague, Soegijapranata returned to Semarang. The post-revolution period was marked by a drastic increase in enrolment at the nation's seminary; the 100th native Indonesian clergyman was ordained in 1956. The government, however, enacted several laws that limited the Church's ability to expand. In 1953 the Ministry for Religion decreed that no foreign missionaries would be allowed into the country, and a subsequent law prohibited those already in Indonesia from teaching. In response, Soegijapranata encouraged eligible clergy to apply for Indonesian citizenship, circumventing the new laws.
Aside from overseeing the new clergy, Soegijapranata continued to work towards Catholic education and prosperity, similar to his pre-war work. He emphasised that students must not only be good Catholics, but also good Indonesians. The Church began further development of its schools, ranging from elementary schools to universities. Soegijapranata also began reforming the Church in his apostolic vicariate, making it more Indonesian. He advocated the use of local languages and Indonesian during mass, allowing it throughout his diocese beginning in 1956. In addition, he pressed for the use of gamelan music to accompany services, and agreed to the use of wayang shows to teach the Bible to children.
As the Cold War heated up, tensions developed between the Church in Indonesia and the Indonesian Communist Party (Partai Komunis Indonesia, or PKI). Soegijapranata believed that the PKI was making progress with the poor through its promises of workers' rights in a communist-led union. To combat this, he worked with other Catholics to establish labour groups, open to both Catholics and non-Catholics. He hoped that these would empower workers and thus limit the PKI's influence. One such labour group was Buruh Pancasila, which was formed on 19 June 1954; through the organisation Soegijapranata helped promote the state philosophy of Pancasila, literally "the five tenets". The following year the Church Representatives Conference of Indonesia (Konferensi Waligereja Indonesia, or KWI), recognising Soegijapranata's devotion to the poor, put him in charge of establishing social-support programmes throughout the archipelago. On 2 November 1955, he and several other bishops issued a decree denouncing communism, Marxism, and materialism, and asking the government to ensure fair and equitable treatment for all citizens. Relations between Indonesia and the Netherlands continued to be poor, specifically in regard to control of West Papua, historically under Dutch control but claimed by Indonesia. Soegijapranata firmly supported the Indonesian position; West Papua was annexed in 1963. 
There was also friction within the Catholic groups, first over Sukarno's 1957 decree that he was president for life and establishment of a guided democracy policy. A faction, led by Soegijapranata, supported this decree, while Catholic Party leader I. J. Kasimo's faction was heavily against it. Sukarno, who had a good working relationship with Soegijapranata, asked the vicar to join the National Council, a request that Soegijapranata refused; he did, however, assign two delegates to the Council, ensuring Catholic representation. This, along with Soegijapranata's support of Sukarno's decree on 5 July 1949 calling for a return to the 1945 constitution, resulted in Bishop of Jakarta Adrianus Djajasepoetra's denunciation of Soegijapranata as a sycophant. However, Soegijapranata was strongly against Sukarno's idea of Nasakom, which based part of the nation's government on communism.
Albertus Soegijapranata