Two series of activated carbons were prepared by chemical activation of three different kinds of agricultural waste: cherimoya (Annona cherimola), fig (Ficus carica) and olive (Olea europaea) woods. KOH and H3PO4 were selected as activating agents. The main differences between these trees are their growth rate and the hardness of the wood. Due to these differences, distinct pore structure, surface areas and chemical composition were found for the different activated carbons prepared. Phosphoric acid-activated samples present a high ash content due to the phosphate formation during the activation process. KOH-activated samples are mainly microporous materials with high surface area and pore volumes. On the contrary, when H3PO4 was used as activating agent, activated carbons are meso-microporous materials. Ash content and micropore structure are limiting factors for the application of activated carbons as electrodes for supercapacitors. The best performance corresponds to KOH-activated samples with high capacitance and energy and power densities. The stability of the electrodes, evaluated by charge–discharge cycling, shows that the KOH-activated carbons have a high cyclic stability up to 12,000 cycles. For H3PO4 samples, the capacitance decreases due to their high ash content and the poor stability of the acidic surface groups.