Flux measurements with the aerodynamic gradient method (AGM) performed with a single analyzer measuring non‐simultaneously at two heights have routinely been conducted. This study investigates the effect of this practice with calculations of single analyzer derived fluxes compared to fluxes derived from simultaneous concentration measurements at two heights for NH3. The results show a mean relative difference of less than 7% for the half‐hour averaging intervals, whereas the relative difference in the cumulative loss of total ammoniacal nitrogen (TAN) is less than 4%. Scatter plots and linear regression show linear behavior with slope and intercept close to one and zero, respectively. The regression coefficients were between 0.913 and 0.966 for the simulations, but with large deviations for the single half‐hour measurement interval. Changes in the starting height and averaging duration at each height for the single analyzer calculations yield small differences, but the effect is minimal compared to the general uncertainty of flux determination with AGM.