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Abstract The genus Encephalartos is entirely endemic to Africa, and like most cycad species, the genus is at risk of extinction. One of the threats jeopardising the future of the genus is reproduction failure, a failure that is still poorly understood. Our objective was to investigate what predisposes Encephalartos species to seed damages through predation, a potential cause of reproduction failure. We collected functional traits of 430 individuals of Encephalartos villosus, as well as data on pre‐dispersal seed predation, habitat type and elevation in the Origi Gorge Nature Reserve, South Africa. Then, we analysed our data by fitting a structural equation model. We found that plants tend to be taller when moving from open to close habitat, whereas plant height tends to increase along elevation. In addition, taller plants tend to have more leaves, and plant canopy size shows significant positive relationship with elevation, plant height and number of leaves. These findings suggest a leaf height–canopy dimension strategy perhaps in response to environmental stresses imposed by elevation. We tested the effects of habitat types on seed production. Although there were significantly more seeds in open habitats, open habitats showed the lowest proportion of predated seeds. Finally, we tested the effects of elevation on seed production. We found that seed production decreases along elevation while the proportion of predated seeds increases. Under the resource concentration hypothesis, these findings (where there are more resources, predation is low) are unexpected, suggesting rather that it is the resource dilution effect that matches the pre‐dispersal seed predation patterns in our study area. We suggest that anthropogenic pressures at lower elevation due to easy access may cause seed predators to shift towards higher elevation where they cause heavier damage to seed, thus perhaps contributing to the extinction risk of the genus Encephalartos.