Vondel was born on 17 November 1587 on the Große Witschgasse in Cologne, Holy Roman Empire. His parents were Mennonites of Antwerpian descent. In 1595 the municipals informed the Mennonites of Cologne that they had to leave the city within fourteen days. The Vondel family was adrift, and went to Frankfurt, Bremen, Emden, and Utrecht, and eventually settled in Amsterdam in the newly formed Dutch Republic. Though the Mennonites were barely tolerated even in Amsterdam, Joost senior acquired citizenship on 27 March 1597, which enabled him to set up a business. He became a silk trader.

In 1606 Vondel was baptized as a Mennonite. The following year his father, who had a silk business in the Warmoesstraat, died, and Vondel was brought in as a business partner.

At the age of 23, Vondel married Mayken de Wolff. Together they had four children, of whom two died in infancy. Around 1620 he must have suffered from depression, with a second period of melancholia occurring in 1626.

During his life, he became one of the main advocates for religious tolerance. After the arrest, trial and the immediate beheading of the most important civilian leader of the States of the Netherlands, Johan van Oldenbarnevelt (1619), at the command of his enemy, Prince Maurits of Nassau, and the Synod of Dort (1618–1619), the Calvinists became the decisive religious power in the Republic. Public practice of Catholicism, Anabaptism and Arminianism was from then on officially forbidden but worship in clandestine houses of prayer was tolerated. Vondel wrote many satires criticising the Calvinists and extolling Oldenbarnevelt. That, together with his new faith, made him an unpopular figure in Calvinist circles. He died a bitter man though he was honoured by many fellow poets, on 5 February 1679.

The Dutch five guilder banknote bore Vondel’s portrait from 1950 until it was discontinued in 1990.