At SMEAR II research station in Hyytiala, located in the Finnish boreal forest, the process of new particle formation and the role of ions has been investigated for almost 20 years near the ground and at canopy level. However, above SMEAR II, the vertical distribution and diurnal variation of these different atmospheric ions are poorly characterized. In this study, we assess the atmospheric ion composition in the stable boundary layer, residual layer, mixing layer, and free troposphere, and the evolution of these atmospheric ions due to photochemistry and turbulent mixing through the day. To measure the vertical profile of atmospheric ions, we developed a tailored set-up for online mass spectrometric measurements, capable of being deployed in a Cessna 172 with minimal modifications. Simultaneously, instruments dedicated to aerosol properties made measurements in a second Cessna. We conducted a total of 16 measurement flights in May 2017, during the spring, which is the most active new particle formation season. A flight day typically consisted of three distinct flights through the day (dawn, morning, and afternoon) to observe the diurnal variation and at different altitudes (from 100 to 3200 m above ground), to capture the boundary layer development from the stable boundary layer, residual layer to mixing layer, and the free troposphere. Our observations showed that the ion composition is distinctly different in each layer and depends on the air mass origin and time of the day. Before sunrise, the layers are separated from each other and have their own ion chemistry. We observed that the ions present within the stable layer are of the same composition as the ions measured at the canopy level. During daytime when the mixing layer evolved and the compounds are vertically mixed, we observed that highly oxidized organic molecules are distributed to the top of the boundary layer. The ion composition in the residual layer varies with each day, showing similarities with either the stable boundary layer or the free troposphere. Finally, within the free troposphere, we detected a variety of carboxylic acids and ions that are likely containing halogens, originating from the Arctic Sea.