East Timorese animist belief systems did not fit with Indonesia's constitutional monotheism, resulting in mass conversions to Christianity.

During the occupation, Bishop Carlos Ximenes Belo became one of the most prominent advocates for human rights in Timor-Leste and many priests and nuns risked their lives in defending citizens from military abuses.

Pope John Paul II's 1989 visit to Timor-Leste exposed the occupied territory's situation to world media and provided a catalyst for independence activists to seek global support.

[10] The pope spoke out against violence in Timor-Leste, and called for both sides to show restraint, imploring the East Timorese to "love and pray for their enemies.

[10] The Catholic Church remains very involved in politics, with its 2005 confrontations with the government over religious education in school and the forgoing of war crimes trials for atrocities against East Timorese by Indonesia.

[18] In 2015, the Salesians of Don Bosco and the Daughters of Mary Help of Christians, with the help of an international relief organization Stop Hunger Now, provided more than 1,100 students across the country with better nutrition through fortified rice-meals.