Objectives We explore physical activity in early farming societies of Central Chile during the Early Ceramic and Late Intermediate Periods (200–1450 CE), a time of technological changes and intensification of food production. The existence of differences in entheseal changes (EC) between females and males is evaluated in two periods with different subsistence strategies. Material and methods EC were recorded with method in the upper and lower limbs of 56 male and female adult individuals from the Early Ceramic Period (ECP) and Late Intermediate Period (LIP). Hierarchical multiple factor analysis and hierarchical clustering on principal components were performed using an exploratory approach. Results In all the analyzed limbs, the EC scores are higher in males than females, which may be explained by sexual dimorphism. A constant overlap in the variability of the EC among males and females is observed. However, the EC scores show a different pattern of variability when comparing ECP females with LIP females. The results show that the scores increase in the latter. In contrast, when comparing ECP males with LIP males scores decrease in the later period. Discussion Physical activity in the societies of Central Chile with incipient agriculture did not vary by sex or during the timeframe studied. Nevertheless, the interaction between sex‐period and the variability pattern of the EC from one period to another suggests different ways of doing similar physical activities or different emphases for similar biomechanical actions.