Climate warming increases the risk of insect defoliation in boreal forests. Losses in photosynthetically active surfaces cause reduction in net primary productivity and often compromise carbon reserves of trees. The concurrent effects of climate change and removal of foliage on root growth responses and carbohydrate dynamics are poorly understood, especially in tree seedlings. We investigated if exposures to different combinations of elevated temperature, CO2, and nutrient availability modify belowground carbon gain and root morphology in artificially defoliated 1-year-old silver birches (Betula pendula). We quantified nonstructural carbohydrates (insoluble starch as a storage compound; soluble sucrose, fructose, and glucose) singly and in combination in fine roots of plants under winter dormancy. Also the total mass, fine root proportion, water content, and length of roots were defined. We hypothesized that the measured properties are lower in defoliated birch seedlings that grow with ample resources than with scarce resources. On average, fertilization markedly decreased both the proportion and the carbohydrate concentrations of fine roots in all seedlings, whereas the effect of fertilization on root water content and dry mass was the opposite. However, defoliation mitigated the effect of fertilization on the root water content, as well as on the proportion of fine roots and their carbohydrate concentrations by reversing the outcomes. Elevation in temperature decreased and elevation in CO2 increased the absolute contents of total nonstructural carbohydrates, whereas fertilization alleviated both these effects. Also the root length and mass increased by CO2 elevation. This confirms that surplus carbon in birch tissues is used as a substrate for storage compounds and for cell wall synthesis. To conclude, our results indicate that some, but not all elements of climate change alter belowground carbon gain and root morphology in defoliated silver birch seedlings.