Pulse modulation of an RF-driven atmospheric pressure plasma jets (APPJs) can be used to control the production of short-lived and long-lived species. This was applied for the production of H2O2 by a humidified He APPJ operating at 13.56 MHz. In addition to H2O2, several species involved in plasma chemistry were measured for the first time using different diagnostic methods applied to the same plasma source and under the same conditions: OH by LIF, H2O2 by FTIR and mass spectrometry and HO2, H2 and O2 by mass spectrometry. The feed gas humidity and dissipated plasma power are control parameters for all species. The highest species densities are found for H2 and O2, medium densities for H2O2 and OH, while the OH radical has the lowest density. Pulse modulation of the RF signal was performed with duty cycles of 10% and 50% and various numbers of pulses per residence time of the gas. With an increasing number of pulses per residence time, an accumulation of the long-lived H2O2 is evident while the formation of the short-lived OH radical is suppressed. H2 and O2 showed remarkable differences when pulse modulation is applied, as the H2 density is reduced by half and the O2 density increases almost fivefold. Thus, the chemistry under pulse modulation of the RF signal is shifted to O-containing chemistry.