Zero-shot voice conversion aims to transform a source speech utterance to match the timbre of a reference speech from an unseen speaker. Traditional approaches struggle with timbre leakage, insufficient timbre representation, and mismatches between training and inference tasks. We propose Seed-VC, a novel framework that addresses these issues by introducing an external timbre shifter during training to perturb the source speech timbre, mitigating leakage and aligning training with inference. Additionally, we employ a diffusion transformer that leverages the entire reference speech context, capturing fine-grained timbre features through in-context learning. Experiments demonstrate that Seed-VC outperforms strong baselines like OpenVoice and CosyVoice, achieving higher speaker similarity and lower word error rates in zero-shot voice conversion tasks. We further extend our approach to zero-shot singing voice conversion by incorporating fundamental frequency (F0) conditioning, resulting in comparative performance to current state-of-the-art methods. Our findings highlight the effectiveness of Seed-VC in overcoming core challenges, paving the way for more accurate and versatile voice conversion systems.