Measurements of the mass concentration and chemical speciation of aerosols are important to investigate their chemical and physical processing from near emission sources to the most remote regions of the atmosphere. A common method to analyze aerosols is to collect them onto filters and analyze the filters offline; however, biases in some chemical components are possible due to changes in the accumulated particles during the handling of the samples. Any biases would impact the measured chemical composition, which in turn affects our understanding of numerous physicochemical processes and aerosol radiative properties. We show, using filters collected onboard the NASA DC-8 and NSF C-130 during six different aircraft campaigns, a consistent, substantial difference in ammonium mass concentration and ammonium-to-anion ratios when comparing the aerosols collected on filters versus an Aerodyne aerosol mass spectrometer (AMS). Another online measurement is consistent with the AMS in showing that the aerosol has lower ammonium-to-anion ratios than obtained by the filters. Using a gas uptake model with literature values for accommodation coefficients, we show that for ambient ammonia mixing ratios greater than 10 ppbv, the timescale for ammonia reacting with acidic aerosol on filter substrates is less than 30 s (typical filter handling time in the aircraft) for typical aerosol volume distributions. Measurements of gas-phase ammonia inside the cabin of the DC-8 show ammonia mixing ratios of 45±20 ppbv, consistent with mixing ratios observed in other indoor environments. This analysis enables guidelines for filter handling to reduce ammonia uptake. Finally, a more meaningful limit of detection for University of New Hampshire Soluble Acidic Gases and Aerosol (SAGA) filters collected during airborne campaigns is ∼0.2 µg sm⁻³ of ammonium, which is substantially higher than the limit of detection of ion chromatography. A similar analysis should be conducted for filters that collect inorganic aerosol and do not have ammonia scrubbers and/or are handled in the presence of human ammonia emissions.