The prompt formation of highly oxidized organic compounds in the ozonolysis of cyclohexene (C6H10) was investigated by means of laboratory experiments together with quantum chemical calculations. The experiments were performed in borosilicate glass flow tube reactors coupled to a chemical ionization atmospheric pressure interface time-of-flight mass spectrometer with a nitrate ion (NO3(-))-based ionization scheme. Quantum chemical calculations were performed at the CCSD(T)-F12a/VDZ-F12//ωB97XD/aug-cc-pVTZ level, with kinetic modeling using multiconformer transition state theory, including Eckart tunneling corrections. The complementary investigation methods gave a consistent picture of a formation mechanism advancing by peroxy radical (RO2) isomerization through intramolecular hydrogen shift reactions, followed by sequential O2 addition steps, that is, RO2 autoxidation, on a time scale of seconds. Dimerization of the peroxy radicals by recombination and cross-combination reactions is in competition with the formation of highly oxidized monomer species and is observed to lead to peroxides, potentially diacyl peroxides. The molar yield of these highly oxidized products (having O/C > 1 in monomers and O/C > 0.55 in dimers) from cyclohexene ozonolysis was determined as (4.5 ± 3.8)%. Fully deuterated cyclohexene and cis-6-nonenal ozonolysis, as well as the influence of water addition to the system (either H2O or D2O), were also investigated in order to strengthen the arguments on the proposed mechanism. Deuterated cyclohexene ozonolysis resulted in a less oxidized product distribution with a lower yield of highly oxygenated products and cis-6-nonenal ozonolysis generated the same monomer product distribution, consistent with the proposed mechanism and in agreement with quantum chemical modeling.