•Five beech forest ecosystems were limed with carbonates 20 to 40 years ago.•Liming reduces acidity, improves soil fertility, tree nutrition and tree growth.•Biological cycling tends to maintain the applied elements in the soil-plant.•Liming with carbonate may cause long term nutrient imbalances in Mg and K. Most forest ecosystems grow on acid and nutrient poor soils. In many cases, a slow degradation of forest soil chemical fertility due to increasing external pressures (decreasing atmospheric inputs, intensification of biomass harvesting and silvicultural practices) has been observed and is a growing concern in the international forest community. When the pressure endured by low fertility forest ecosystems is too intense, nutrient losses and ecosystem function losses may occur, forest decline being the ultimate stage of this process. In such cases, forest liming with a carbonate product is a solution to restore soil fertility and reduce soil acidity, globally improve the ecosystem functioning and compensate for nutrient losses caused by biomass harvest and exportation. However, the effects of liming on ecosystem processes and the biogeochemical cycling of nutrients in forest ecosystems are still unclear. We studied the dynamics of magnesium and calcium originating from the dissolution of liming products in the different compartments (organic and mineral soil layers and, aboveground biomass) of five long-term (20 to 40 years) monitoring beech (Fagus sylvatica L.) plots located in Northern France from ecosystem magnesium and calcium budgets. Compared to the control plots, soil exchangeable pools of Mg and Ca in the 0–15 cm mineral soil layer increased during the first decade after liming but these differences rapidly decreased after 20–30 years. The effect of liming on foliar concentrations and tree growth was still observed after 40 years, most probably because the biological cycling of these elements was more dynamic in the limed plots. Liming increased the decomposition rate of the soil organic layer but the pools of Mg and Ca in this layer remained relatively stable over time, probably because Mg and Ca concentrations in foliage and litterfall increased after the liming. Liming effects varied between sites depending on the liming product and amount, and the initial chemical fertility level of the soil. Although liming operations may help improve forest soil fertility, they may also generate nutrient deficiencies and/or imbalances for nutrients that are poorly available in the soil. The planning of liming operations therefore necessitates a thorough soil chemical fertility diagnosis.