We present an electrospray ion source coupled to an orthogonal continuous-flow atmospheric pressure chemical ionization region. The source can generate intense and stable currents of several specific reagent ions using a range of salt solutions prepared in methanol, thereby providing both an alternative to more common radioactive ion sources and allowing for the generation of reagent ions that are not available in current chemical ionization mass spectrometry (CIMS) techniques, such as alkaline cations. We couple the orthogonal electrospray chemical ionization (ESCI) source to a high-resolution time-of-flight mass spectrometer (HR-ToF-MS), and assess instrument performance through calibrations using nitric acid (HNO3), formic acid (HCOOH), and isoprene epoxydiol (trans-β-IEPOX) gas standards, and through measurements of oxidized organic compounds formed from ozonolysis of α-pinene in a continuous-flow reaction chamber. When using iodide as the reagent ion, the HR-ToF-ESCIMS prototype has a sensitivity of 11, 2.4, and 10 cps pptv−1 per million counts per second (cps) of reagent ions and a detection limit (3σ, 5 s averaging) of 4.9, 12.5, and 1.4 pptv to HNO3, HCOOH, and IEPOX, respectively. These values are comparable to those obtained using an iodide-adduct HR-ToF-CIMS with a radioactive ion source and low-pressure ion–molecule reaction region. Applications to the α-pinene ozonolysis system demonstrates that HR-ToF-ESCIMS can generate multiple reagent ions (e.g., I−, NO3−, acetate, Li+, Na+, K+, and NH4+) having different selectivity to provide a comprehensive molecular description of a complex organic system.