Over the last decades, micro-archaeological and ethnoarchaeological approaches have demonstrated the importance of animal dung deposits for reconstructing past human lifeways, primarily within caves and rock-shelters. The case study of Tossal de Baltarga (eastern Pyrenees) provides evidence from simultaneous storage and penning, along with the in situ remains in anatomical connection of several ovicaprines and a horse within a building destroyed by fire, dating to the second half of the third century BC. The current study provides new evidence for animal management and organisation of space at the site through examination in micromorphological thin-section and integrated phytolith and dung spherulite analyses. Micromorphological results reveal spatial variations in dung accumulation, possibly related to differences in the use of space. Phytolith records further provide insights into herbivorous regimes, dominated by a range of grass matter suggested to derive from fodder and/or grazing through the penning lifetime. This integrated approach contributes to the understanding of depositional pathways and taphonomy of penning deposits within built environments, critical for the reconstruction of activity areas and practices related to animal management, foddering/grazing patterns, site formation processes, concepts of space within the settlement, health and the complexity of interactions between people and animals in mountain areas.