Transmission electron microscopy (TEM) is a tool used to image, in good resolution, the structure of organelles within the cell. Available protocols are designed to image structures within fixed intact cells. Here, we described a protocol where Golgi, isolated from cells by GolgiTAG immunoprecipitation (IP) (as described in ddx.doi.org/10.17504/protocols.io.6qpvrdjrogmk/v1), can be prepared and imaged using TEM. This protocol can also be used to image any organelles isolated using various organelle-IP protocols that are available.