The precipitation of energetic particles is a source of ionization in the atmosphere and ionosphere. Variations in ionization are associated with the intensity of the precipitating particle flux during solar eruptive events and geomagnetic disturbances. Chains of chemical reactions are triggered in both the atmosphere and ionosphere, which can lead to abrupt changes in both the chemical composition of the atmosphere and the electron concentration in the ionosphere. In this paper, we study the variability of the electron concentration in the D layer of the high-latitude ionosphere and changes in the main chemical components of the atmosphere leading to ozone depletion, depending on the intensity of the particle flux. All presented results were obtained through numerical modeling using a one-dimensional radiative-convective photochemical model, which includes interactive blocks for the chemistry of both neutral and ionized components. This integrated approach allows for a highly accurate reproduction of the inextricable link between physical disturbances and subsequent chemical responses in the atmosphere–ionosphere system.