Rather than simply an arena for Euroamerican domination, recent archaeological research on Spanish missionization along the North American Borderlands points to opportunities for indigenous autonomy under missionary colonialism. We build from these discussions to foreground autonomy as it was expressed in multiple spatial contexts during the colonial period (ca. 1770s–1850s) in central California. Our goals are to evaluate freedom of action within the situational constraints imposed by Spanish missions in California and also to challenge archaeologists to move beyond prevailing narratives of decline to critically assess how native people negotiated colonialism across the landscape. Drawing on three archaeological examples from central California—including Mission Santa Clara de Asís, the marshlands of the San Joaquin Valley, and persistent Coast Miwok villages in the northern San Francisco Bay region—we outline a conceptual model comprised of three spatial zones: colonial settlements as native places; native homelands/colonial hinterlands; and interior worlds and interspaces. The model offers a way in which to expand mission archaeology by illuminating the opportunities for indigenous autonomy in social, political, and economic relationships that intersected colonial modes in various ways across time and space.