He was entrusted with the Xth Department for Agricultural-Zoological Research,[1] and in 1894 he established the Landbouw Zoologish (now the Bogor Zoology Museum).

[1] Between 1915 and 1916, he acted on behalf of Hermanus Johannes Lovink as the director of the Indies' Department of Agriculture, Industry, and Trade; he wrote that he preferred his position with the Lands Plantentuin, as it had fewer administrative challenges.

[7] In his capacity as the director of the Lands Plantentuin, Koningsberger regularly interacted with the Governors-General of the Dutch East Indies, including Alexander Idenburg and Johan Paul van Limburg Stirum.

[1] According to the Dutch historian Wim van den Doel [nl], this leadership was unsuccessful; Koningsberger was uncomfortable with his role, and perceived by the Governor-General as failing to direct discussions within the body.

[1] Following the flu epidemic of 1918, which afflicted Koningsberger as well as thousands in Java, he decided to return to the Netherlands with his family.

In a 1925 speech, he emphasized that the Netherlands required an ethical policy both to pay its debt of honour to the indigenous population and to acknowledge the growing sense of nation in the colony.

[8] On 26 March, he appointed Andries Cornelis Dirk de Graeff the Governor-General of the Dutch East Indies.

Feeling too distanced from the contemporary situation in the Indies to make effective policy, he entrusted most issues to de Graeff and sought to avoid conflict.

[1] Even as he opened these opportunities, he continued to espouse the importance of maintaining Dutch leadership, rejecting the idea of departing from Western codes of law in favour of certain population groups.

[1] Koningsberger's son Victor was a professor of botany in Utrecht,[8] specializing in plant physiology; he was also the president of the Royal Tropical Institute in Amsterdam.