This study investigates the vulnerability of long-span suspension bridges to spatially variable vertical ground motions (SV-VGMs). While of recognized importance, a comprehensive understanding of this topic has been traditionally limited by the unavailability of an adequate number of arrays of motions. In this work, 10 simulations of a large-magnitude Hayward Fault earthquake are utilized to perform site-specific structural response assessments of a suspension bridge under different load scenarios. A detailed nonlinear model representative of the West San Francisco-Oakland Bay Bridge is employed as the case study structure. Four sets of nonlinear time-history analyses are performed with and without VGMs and with and without the incorporation of spatial variability to offer the basis for a complete comparison of the demand distributions across different load cases. Results indicate that VGMs largely influence the response of the bridge decks in the vertical direction, with an increase in drifts up to 2× for the case of synchronous input and up to 2.5× for the case of asynchronous inputs. The analysis of the bridge response in the time and frequency domain across all load cases reveals a high sensitivity of the decks’ response to minor time lags in input motions of comparable amplitude, which are seen to activate the contribution of higher modes to the structural response. Evidence from this study points to the potential of severely underestimating structural demands if the (even limited) spatial variability of the input motions is not incorporated correctly. For the case study structure, the probability of exceeding the onset of nonlinearity in the short decks at the design earthquake level is seen to increase by a factor of about two when considering SV-VGMs as opposed to synchronous horizontal motions only.