Arriving in early 1803, he attempted to strengthen the defences of the colony, but found resources lacking, having few trained troops at his disposal and the political situation tenuous at best.

When he returned to the Netherlands, Napoleon had already installed his brother Louis Bonaparte as the king of the newly formed Kingdom of Holland.

He held a series of high-ranking administrative posts within the kingdom until the abdication of Louis Napoleon and the annexation of the Netherlands by France in 1810.

On 11 November 1810, he was appointed governor-general of the territory known, before the annexation, as the Dutch East Indies, replacing Herman Willem Daendels.

A large number of French soldiers were captured during the retreat and ensuing pursuit and Janssens was forced to surrender on 18 September 1811.

In mid-March 1814, Janssens collected 3,600 French soldiers from various garrisons and successfully marched through Allied-held territory to join Napoleon at Reims.