Organic peroxide explosives (OPEs) are unstable, non-military, contemporary security threats often found in improvised explosive devices. Chemiluminescence (CL) can be used to detect OPEs, via radical formation consisting of peroxide moieties (-O-O-) under acidic conditions. However, selectivity for specific OPEs is hampered by the ubiquitous background of H2O2. Herein, we report the differentiation of hexamethylene triperoxide diamine (HMTD), triacetone triperoxide (TATP), and methyl ethyl ketone peroxide (MEKP) by specific flow injection analysis–CL (FIA-CL) signal profiles, after H2SO4 treatment. The radical degradation pathway of each structure, and its corresponding FIA-CL profile, was explored using mass spectrometry to reveal the rapid loss of -O-O- from TATP and HMTD structures, while MEKP formed CL signal-sustaining oligomers, as opposed to the immediate attenuation of H2O2. The CL response for OPEs in an aqueous media, measured via the described FIA-CL method, enabled ultra-trace limits of detection down to 0.40 μM for MEKP, 0.43 μM for HMTD, and 0.40 μM for TATP (combined linear range 1–83 μM with 95% confidence limit, n = 12). Expanded uncertainties of measurement (UM) of MEKP = ±0.98, HMTD = ±1.03, and TATP = ±1.1 (UM included probabilities of false positive and false negative as well as standard deviations of % recoveries and limit of detections of OPEs). Direct aqueous sample introduction via FIA-CL thus offers the prospect of rapid and selective screening of OPEs in security-heightened settings (e.g., airports), averting false positives from more ubiquitous H2O2.