Mismatch negativity (MMN) event-related potential (ERP) component reduction, indexing N-methyl-D-aspartate receptor (NMDAR)-dependent auditory echoic memory and short-term plasticity, is a well-established biomarker of schizophrenia that is sensitive to psychosis risk among individuals at clinical high-risk (CHR-P). Based on the NMDAR-hypofunction model of schizophrenia, NMDAR-dependent plasticity is predicted to contribute to aberrant neurodevelopmental processes involved in the pathogenesis of schizophrenia during late adolescence or young adulthood, including gray matter loss. Moreover, stress and inflammation disrupt plasticity. Therefore, using data collected during the 8-center North American Prodrome Longitudinal Study (NAPLS-2), we explored relationships between MMN amplitudes and salivary cortisol, gray matter volumes, and inflammatory cytokines. Participants included 303 CHR-P individuals with baseline electroencephalography (EEG) data recorded during an MMN paradigm as well as structural magnetic resonance imaging (MRI) and salivary cortisol, of which a subsample (n = 57) also completed blood draws. More deficient MMN amplitudes were associated with greater salivary cortisol and pro-inflammatory cytokine levels in future CHR-Converters, but not among those who did not convert to psychosis within the next two years. More deficient MMN amplitude was also associated with smaller total gray matter volume across participants regardless of future clinical outcomes, and with subcortical gray matter volumes among future CHR-Converters only. These findings are consistent with the theory that deficient NMDAR-dependent plasticity results in an overabundance of weak synapses that are subject to over-pruning during psychosis onset, contributing to gray matter loss. Further, MMN plasticity mechanisms may interact with stress, cortisol, and neuroinflammatory processes, representing a proximal influence of psychosis.