Capacitive deionization (CDI) is a desalination technology that shows promise for removing nitrate and phosphate ions. The main components of CDI cells are electrodes, which are typically made from activated carbon (AC). However, the electrosorption performance of AC electrodes is limited because of the negative zeta potential, hydrophobicity, and oxidation resulting in co–ions’ repulsion. This study investigates binder-free polypyrrole-coated nanocellulose (NC/PPy) electrodes, which are hydrophilic and possess various functional groups, as an alternative to AC electrodes. An asymmetric CDI cell with an NC/PPy positive electrode demonstrated greater energy and charge efficiencies compared to a symmetric cell. The NC/PPy electrode exhibited a threefold electrosorption capacity towards nitrate ions compared to the AC electrode, and 4.5 times higher than for phosphate ions. The electrosorption mechanism revealed by first-principles modeling indicates similar sorption energies for nitrate and phosphate ions, with higher nitrate capacity due to co-ion repulsion and diffusion effects.