Coffee brew flavor is known to degrade during storage. Untargeted and targeted LC/MS flavoromics analysis was applied to identify chemical compounds generated during storage that impacted the flavor stability of ready-to-drink (RTD) coffee. MS chemical profiles for sixteen RTD coffee samples stored for 0, 1, 2, and 4 months at 30 °C were modeled against the sensory degree of difference (DOD) scores by orthogonal partial least squares (OPLS) with good fit and predictive ability. Five highly predictive untargeted chemical features positively correlated to DOD were subsequently identified as 3-caffeoylquinic acid, 4-caffeoylquinic acid, 5-caffeoylquinic acid, 3-O-feruloylquinic acid, and 5-O-feruloylquinic acid. The increase in the six acidic compounds during storage was confirmed by sensory recombination tests to significantly impact the flavor stability of RTD coffee during storage. A decrease in pH, rather than an increase in total acidity, was supported to impact the coffee flavor profile.