Born in Enschede, Holland, the youngest of three brothers. He attended the Gymnasium St. Jacobuscollege in Enschede and was the editor of school paper 't Komkommertje. Graduated in 1987. Thanks to excellent grades, he was allowed to apply for a scholarship in the USA. He also contributed to the Dutch gay newspaper de Gay Krant, and the political journal Vrij Nederland.
He studied Liberal arts at Hampshire College in Amherst, Massachusetts. After one year he was granted a second scholarship for another 3 years, and he decided to stay. He studied English literature and modern Russian history . He learned to speak, read and write Russian fluently. He graduated in 1992 with a degree in Russian and post-Soviet studies. He then became a researcher in the Moscow bureau of the Financial Times in London. Two months later he was given a job by the English-language Moscow Times.
In 1996 he went to Kazakhstan as the Financial Times's central Asia correspondent. Deciding that his next station would be Indonesia, he went to take courses in Indonesian culture and contemporary history and a language course in Bahasa Indonesia.
In September of 1997 he went to live in Jakarta. In two years, he wrote 608 articles for the Financial Times and contributed regularly to the Christian Science Monitor (Boston, USA), Vrij Nederland and Radio Deutsche Welle (Germany). Covered the proces of change and chaos following the downfall of dictator Soeharto, from all over Indonesia. He also did some reporting for Marketplace, a radio program on National Public Radio focusing on national/international business.
In December of 1998 he got to know Ian Nugrahane over the internet and they became lovers. In April of 1999 he visited the Netherlands for the last time for his brother's wedding, for which he was best man. Sander proposed Ian to get married legally in Holland a week before he died.
While covering events in Dili, East Timor, he was riding on a motorcycle taxi in the suburb of Becora. According to the driver six uniformed gunmen riding three motorcycles ordered them to stop. When they drove off the gunmen opened fire. Sander Thoenes died at the scene, and his body was recovered by Australian soldiers who also found his reporter's notebook and pen by his hand.
His boyfriend Ian survived him in Jakarta where they had lived together.