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In this chapter, the authors review how integrated microstratigraphic, phytolith and chemical analyses can contribute to our understanding of continuity and change in ecological and social practices during the transition to agriculture, in Zagros, with selective comparative reference to central Anatolia. They examine how micro-contextual analysis of plant materials preserved in large thin-sections and phytolith analyses are contributing to a fuller understanding of the ecology and use of both wild and domesticated plants than is possible from study of charred plants alone. They consider how integrated analyses of animal dung are informing on the earliest stages of animal management, including penning, foddering and use of dung for fuel. Lastly they briefly review the microstratigraphic evidence for how the transition to agriculture was shaped by and impacted on particular activities, roles and relations within households and communities by study of continuity and change in the nature, timing and organisation of these.