Oxygenated organic molecules (OOMs) formed from oxidation of anthropogenic and biogenic volatile organic compounds (VOCs) are essential ingredients for atmospheric new particle formation (NPF) and secondary organic aerosol (SOA) formation, and thus impact air quality, human health, and climate. There is a large variety of OOM compounds, but currently, for the vast majority of OOMs, their molecular structures and formation pathways are still unknown. In this study, we identified isomer-resolved molecular structures and reaction pathways for dimer OOMs formed from ⍺-pinene ozonolysis, using an ultrahigh-performance liquid chromatography-electrospray ionization Orbitrap mass spectrometer (UPLC/(-)ESI-Orbitrap MS) tandem analysis and a high-resolution time-of-flight chemical ionization mass spectrometer (HrTOF-CIMS) attached to the filter inlet for gas and aerosol (FIGAERO), combined with explicit chemical modeling simulations using the Generator of Explicit Chemistry and Kinetics of Organics in the Atmosphere (GECKO-A). In general, each OOM identified in the newly formed biogenic particles contains 2–8 isomers with distinctive MS/MS fragmentation ions. For C₁₉H₃₀O₅, which is one of most abundant dimers identified from the boreal forests and laboratory biogenic NPF studies, one isomer forms in the gas phase from a stabilized Crigee Intermediate (sCI) peroxy biradical and aldehyde, followed by subsequent gas-to-particle conversion; and another isomer forms in the particle phase via the Baeyer-Villiger reaction from a cyclic acylperoxyhemiacetal and ⍺-pinanediol. Two isomers of C₁₆H₂₆O₆ form in the particle phase via decarboxylation from two different isomers of C₁₇H₂₆O₈ after the condensation from the gas phase. Thus, our results show that biogenic OOMs can also form from particle-phase reactions and have different isomeric structures than in the gas phase. Our study represents the first molecular-level chemical analysis to identify particle-formation pathways for OOMs in the newly formed biogenic nanoparticles. Currently, parameterizations of NPF (e.g., biogenic NPF) are based on the gas-to-particle conversion of extremely low-volatility OOM dimers that form in the gas phase alone (e.g., via RO₂ + RO₂ reactions). Our study demonstrates that additional, independent particle-phase formation pathways should also be considered for predictions of the formation and growth of new particles in the atmosphere.