Heavy metals and arsenic contamination in municipal solid waste (MSW) and its treatment products has garnered increasing attention. This study investigated the heavy metals and arsenic flows in organic fractions of MSW (OFMSW) in Shanghai, China, through a one-year monitoring program. The OFMSW separated directly from the source (source-separated, pure organic waste), obtained from the treatment facilities were sampled and compared with pure foodstuffs. The heavy metals and arsenic contents in the source-separated OFMSW resembled those in foodstuffs, whereas the OFMSW from the treatment facilities was significantly contaminated with heavy metals and arsenic and failed to meet the government standards for land use. Using flow analysis, > 80% of heavy metals and arsenic were from extrinsic inorganic waste with high ash content that was combined with OFMSW during MSW collection, transfer, transportation, and storage stages. Based on source analysis of heavy metals and arsenic, suggestions for reducing heavy metals and arsenic contents in the current MSW management system in Shanghai are presented.