As director of the Philips factories in Lithuania and part-time acting consul of the Dutch government-in-exile, he supervised the writing of 2,345 visas for Curaçao to save Jews from the Holocaust during World War II.

Zwartendijk was authorized or instructed by his superior, Ambassador to Latvia L. P. J. de Decker, to issue the same modified text to Jews who wished to escape from Lithuania.

In the three weeks after 16 July 1940, Jan Zwartendijk, honorary Dutch consul, wrote 2,345 passport inscriptions to Curaçao and some of the Jews copied more.

[10] In 2018 Dutch author Jan Brokken published De Rechtvaardigen ('The Just'), a book describing the rescue operation and Zwartendijk's life.

Though the novel does not mention these men by name, it describes a "Dutch consul in Kovno who was madly issuing visas to Curaçao, in league with a Japanese official who would grant rights of transit" (p. 65).

In 2022, the monument Loom Light created by Titia Ex was unveiled in Eindhoven, the Netherlands, in commemoration of Zwartendijk and regional resistance fighters.