Flight routes of commercial aircraft are adjusted to the actual meteorological situation in order to benefit from tail winds and avoid head winds and dangerous flight conditions. This study investigates whether these adjustments have an impact on the partitioning and the residence times of aircraft emissions in the stratosphere and troposphere. A Lagrangian dispersion model is used in combination with a mean emission inventory and emissions along actual flight tracks. Both inventories are established from Measurement of Ozone and Water Vapor by Airbus In-Service Aircraft (MOZAIC) aircraft position data in the North Atlantic Flight Corridor (NAFC) over a 1-year period. The results show that stratospheric emissions released in the NAFC are transported in a northeasterly direction towards polar regions on a timescale of a few days. The mean residence time of these emissions is about 23 days, which is shorter than documented in previous studies. The greatest fluxes from the stratosphere into the troposphere occur during the first 10 days and have their maxima over Europe and North Africa. About 62% and 67% of the emissions are directly deposited in the stratosphere in the mean emission inventory and in the inventory of the actual flight tracks, respectively. The deposition in the stratosphere was found to be sensitive to the definition of the tropopause height. However, the transport and partitioning of the emissions in the stratosphere and troposphere are only moderately affected if an inventory of the actual flight tracks is used instead of a mean emission inventory. Therefore, the systematic errors made in chemistry climate models, which use mean inventories, are small and can be tolerated for most applications.