If Jupiter and the Sun both formed directly from the same well-mixed proto-solar nebula, then their atmospheric compositions should be similar. However, direct sampling of Jupiter’s troposphere indicates that it is enriched in elements such as C, N, S, Ar, Kr, and Xe by 2–6× relative to the Sun (Wong, M.H., Lunine, J.I., Atreya, S.K., Johnson, T., Mahaffy, P.R., Owen, T.C., Encrenaz, T. [2008]. 219–246). Most existing models to explain this enrichment require an extremely cold proto-solar nebula which allows these heavy elements to condense, and cannot easily explain the observed variations between these species. We find that Jupiter’s atmospheric composition may be explained if the Solar System’s disk heterogeneously accretes small amounts of enriched material such as supernova ejecta from the interstellar medium during Jupiter’s formation. Our results are similar to, but substantially larger than, isotopic anomalies in terrestrial material that indicate the Solar System formed from multiple distinct reservoirs of material simultaneously with one or more nearby supernovas (Trinquier, A., Birck, J.-L., Allegre, C.J. [2007]. Astrophys. J. 655, 1179–1185). Such temporal and spatial heterogeneities could have been common at the time of the Solar System’s formation, rather than the cloud having a purely well-mixed ‘solar nebula’ composition.