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Guiding pretrained flow-based generative models for conditional generation or to produce samples with desired target properties enables solving diverse tasks without retraining on paired data. We present ESS-Flow, a gradient-free method that leverages the Gaussian prior of the source distribution in flow-based models to perform Bayesian inference directly in the source space using elliptical slice sampling. ESS-Flow only requires forward passes through the generative model and observation process, making it applicable even when gradients are unavailable, such as with non-differentiable simulation-based observations or quantization in the generation process. We demonstrate its effectiveness on scientific applications including generating materials with target properties, protein backbone structures with improved designability, and synthesizable, drug-like molecules.