We hypothesized that female and male individuals of the dioecious tree species, Juniperus communis, exhibit different strategies of resource allocation when growing under stress conditions. To test this hypothesis, we performed a two-year pot experiment on plants exposed to different levels of nutrient availability. Analysis of the plants revealed a higher concentration of carbohydrates, carbon, and phenolic compounds in needles of female plants, indicating that females allocate more resources to storage and defense than males. This difference was independent of nutrient availability. Differences in carbohydrates levels between the sexes were most often significant in June, during the most intensive phase of vegetative growth in both sexes, but could also be attributed to female resources investment in cone development. A higher level of nitrogen and other macroelements was observed in males than in females, which may have been connected to the accumulation of resources (nitrogen) for pollen grain production in males or greater allocation of these elements to seeds and cones in females. The interaction between sex and soil fertilization for the C:N ratio may also indicate sex-specific patterns of resource allocation and utilization, which is impacted by their availability during specific periods of J. communis annual life cycle.