This Chinese language article from Fu-jen University on the history of missionary work in Taiwan answers the question well. I'll list the main points of the article below.

Missionary work in Taiwan began as early as the 16th century by both Catholic and Protestant missionaries. Spanish missionaries began arriving from the Philippines in 1619 but in 1626 Spain established a foothold in the north of Taiwan and started converting the local population. The Dutch arrived at about the same time and were active around the Tainan area, in the south. The Dutch drove the Spanish out of Taiwan in 1642, but were themselves driven out by Koxinga in 1661. Most converts at this time were plains aborigines, nations which no longer exist, having been destroyed or assimilated into the Han population that started arriving with the Europeans as labourers and later with Koxinga. We have surviving copies of the Siraya translation of the Gospel of Matthew from this period, made by the Dutch.

Later Taiwan was annexed by the Qing Empire, and a second wave of missionary activity began after the Opium Wars that opened Qing China to Western missionary activity. That continued throughout the period of Japanese rule (1895-1945), and during the RoC era.

Catholic conversion rates grew steadily after WW2, from 10900 Catholics in 1945, to over 300 thousand in 1968, but slowed significantly after that (it was still around 300 thousand in 1997). The initial growth can be attributed to the arrival of Catholics from China with the KMT after the Nationalists' loss in the Chinese Civil War, as well as conversions of the newly arrived Mainlanders and, most importantly, the Formosan aboriginal people embracing Christianity, who represented a third of all Catholics in Taiwan despite constituting only 2% of the total population.

Likewise, the Protestant conversion rates were high from the end of the war until the mid 60s, but did pick up somewhat after the mid 70s, growing to a total of 422 thousand believers spread across 52 different denominations, with the Presbyterian Church and True Jesus Church being the biggest. The Protestant churches concentrated their missionary activity in the mountains (Formosan aboriginal nations territory) from 1945-1960, and after that started working mostly with the Min-nan majority (missionary work among the Hakka was largely unsuccessful).

The comparative lack of converts among the Min-nan and Hakka peoples is explained by a very strong connection to Sinitic and Buddhist religious tradition and their stable position in Taiwan, as well as a growing trend of urbanization. Aboriginal people, on the other hand, were marginalized, had disparate religious beliefs (there are 16 officially recognized nations now, and most had their own religious traditions before converting), and lived in remote mountainous areas. Proportionally speaking, a very large number of two main minority groups converted to Christianity: the Formosan aboriginal peoples and the Mainlanders (who came to Taiwan with the KMT in 1949 or after). Conversion rates slowed down significantly in the 60s because by then the largest pool of new converts -- the Formosan aboriginal nations -- were already largely Christian.

Edit: grammer.