In Amsterdam he became interested in navigation and cartography and, having access to nautical charts recently brought from Portugal, he was soon recognized as an expert on safe maritime routes to India and the nearby "spice islands".

Plancius prepared the map, Exacta & accurata delinatio… regionibus China, Cauchinchina, Camboja, sive Champa, Syao, Malacca, Arracan & Pegu, published in Jan Huygen van Linschoten's popular book, Itinerario (1596).

In 1595 Plancius trained Pieter Dirkszoon Keyser, the chief pilot on the Hollandia, to make astronomical observations to fill in the blank area around the south celestial pole on European maps of the southern sky.

These stars appear as 12 new southern constellations,[4] on a 35-cm celestial globe designed by Plancius in late 1597 (or early 1598) and produced in collaboration with the Amsterdam cartographer Jodocus Hondius the Elder.

The 12 new constellations (mostly referring to animals and subjects described in natural history books and travellers' journals of his day) are Apis the Bee (later changed to Musca by Lacaille), Apus the Bird of Paradise, Chamaeleon, Dorado the Goldfish (or Swordfish), Grus the Crane, Hydrus the Small Water Snake, Indus the Indian, Pavo the Peacock, Phoenix, Triangulum Australe the Southern Triangle, Tucana the Toucan, and Volans the Flying Fish.