The VOC nevertheless has a shaping influence in the archipelago.

In what today is eastern Indonesia, the company—with, it is important to reiterate, the help of indigenous allies—between 1610 and 1680 fundamentally alters the terms of the traditional spice trade by forcibly limiting the number of nutmeg and clove trees, ruthlessly controlling the populations that grow and prepare the spices for the market, and aggressively using treaties and military means to establish VOC hegemony in the trade.

One result of these policies, exacerbated by the late-seventeenth-century fall in the global demand for spices, is an overall decline in regional trade, an economic weakening that affects the VOC itself as well as indigenous states, and in many areas occasions a withdrawal from commercial activity.

Others are the rise of authoritarian rulers dependent on VOC support and unrest among groups—traditional leaders, merchants, religious and military figures—who oppose one or the other or both.

Among the most prominent examples are those found in the histories of Ternate in the time of Sultan Mandar (r. 1648-75) and the wars against Hitu and Hoamoal (1638-56), and of southern Sulawesi in the era of the ambitious Buginese (Bone) prince Arung Palakka (1634-96) and the wars against the Makassarese (Gowa) and others.

By the end of the seventeenth century, the glories of the spice trade have faded, and the vitality of the large and small states of the post-Majapahit era has been sapped; the weight of affairs has again begun to shift west, to Java.