Leafcutter ants farm a fungal cultivar (Leucoagaricus gongylophorus) that converts inedible vegetation into food that sustains colonies with millions of workers. Like fruits of crops domesticated by humans, L. gongylophorus has evolved specialized nutritional rewards—tiny swollen hyphal cells called gongylidia that package metabolites eaten by ant farmers. Yet, little is known about how gongylidia form, and whether ants regulate this formation through plant-fragment provisioning. We used microscopy and in vitro manipulations to explain the cellular mechanisms governing gongylidium formation. First, L. gongylophorus is polykaryotic (up to 17 haploid nuclei/cell) and our results suggest intracellular nucleus distributions govern gongylidium morphology with their absence in expanding edges arresting apical growth and their presence mediating complex branching patterns. Second, nanoscale TEM imaging shows that the cultivar recycles its own cellular material (e.g. cytosol, mitochondria) through a process called ‘autophagy’ and stores the resulting metabolites in gongylidia. This autophagic pathway is further supported by gongylidium inhibition when isolated fungal cultures are grown on media with autophagy inhibitors (chloroquine, 3-methyladenine). We hypothesize that autophagic nutritional reward production is the ultimate cultivar service and reflects a higher-level organismality adaptation enabled by strict symmetric lifetime commitment between ant farmers and their fungal crop.