Background: Although elevated [CO2] causes an increase of photosynthesis in the short-term, this increase is often attenuated over time due to decreased photosynthetic capacity of the leaf in a process called photosynthetic acclimation to elevated CO2 (PAC). PAC is often accompanied by N deficiency and sink:source imbalance. The aim of this study is to investigate mechanisms that lead to PAC, N deficiency and sink:source imbalance in tomato plants grown in elevated [CO2] and how they are affected by different levels of N treatments. Methods: Two long-term experiment and two short-term experiments were conducted in which tomato plants were grown in chambers with ambient [CO2] and elevated [CO2] combined with different levels of N nutrition. The following parameters were measured: 1) Biomass 2)Leaf N, P and K concentrations, 3) leaf NO3 − concentration, 4) Gas exchange 5) Rubisco expression and 6) Leaf starch concentration. Results: Plants grown at e[CO2] had increased biomass and starch, and decreased gas exchange, stomatal conductivity, Rubisco expression, Vcmax, NPK and leaf NO3 −. Increasing N fertilization counteracted many of the effects of elevated [CO2]. Conclusions: PAC was caused by decreased N uptake or transport coupled with increased growth which leads to N deficiency and a sink:source imbalance. Increased N fertilization counteracted the effect of e[CO2] on photosynthesis, N status, and sink:source imbalance. Furthermore, elevated [CO2] caused stomata to partially close, which accounted for some of the PAC observed. © 2018, Springer Nature Switzerland AG.