This paper presents a preliminary study combining macrobotanical and phytolith analyses to explore crop processing at archaeological sites in Haryana and Rajasthan, northwest India. Current understanding of the agricultural strategies in use by populations associated with South Asia’s Indus Civilisation (3200–1900 bc) has been derived from a small number of systematic macrobotanical studies focusing on a small number of sites, with little use of multi-proxy analysis. In this study both phytolith and macrobotanical analyses are used to explore the organisation of crop processing at five small Indus settlements with a view to understanding the impact of urban development and decline on village agriculture. The differing preservation potential of the two proxies has allowed for greater insights into the different stages of processing represented at these sites: with macrobotanical remains allowing for more species-level specific analysis, though due to poor chaff presentation the early stages of processing were missed; however these early stages of processing were evident in the less highly resolved but better preserved phytolith remains. The combined analyses suggests that crop processing aims and organisation differed according to the season of cereal growth, contrary to current models of Indus Civilisation labour organisation that suggest change over time. The study shows that the agricultural strategies of these frequently overlooked smaller sites question the simplistic models that have traditionally been assumed for the time period, and that both multi-proxy analysis and rural settlements are deserving of further exploration.