Direct solid analysis of ultrathin layers is investigated using pulsed radiofrequency (rf) glow discharge (GD) time-of-flight mass spectrometry (TOFMS). In particular, previous studies have always integrated the detected ion signals in the afterglow region of the rf-GD pulse, which is known to be the most sensitive one. Nevertheless, the analytical capabilities of other pulse time regions have not been evaluated in detail. Therefore, in this work, we investigate the analyte prepeak region, which is the pulse region where the analyte ions peak after the initial sputtering process of each GD pulse, aiming at obtaining improved depth profile analysis with high depth resolution and with minimum polyatomic spectral interferences. To perform these studies, challenging ultrathin Si–Co bilayers deposited on a Si substrate were investigated. The thickness of the external Si layer was 30 nm for all the samples, whilst the internal Co layer thicknesses were 30, 10, 5, 2 and 1 nm, respectively. It should be remarked that the top layer and the substrate have the same matrix composition (Si > 99.99%). Therefore, the selected samples are suitable to evaluate the response of the Si ion signal in the presence of an ultrathin Co layer as well as the possible oxygen contaminations or its reactions. Additionally, these samples have been evaluated using time-of-flight secondary ion mass spectrometry, and the results compare well to those obtained by our pulsed rf-GD time-of-flight mass spectrometry results.