A method of manufacturing a diamond substrate includes: forming an ion implantation layer at a side of a main surface of a diamond seed substrate by implanting ions into the main surface of the diamond seed substrate; producing a diamond structure by growing a diamond growth layer by a vapor phase synthesis method on the main surface of the diamond seed substrate, after implanting the ions; and performing heat treatment on the diamond structure. The performed heat treatment causes the diamond structure to be separated along the ion implantation layer into a first structure including the diamond seed substrate and failing to include the diamond growth layer, and a diamond substrate including the diamond growth layer. Thus, the method of manufacturing a diamond substrate is provided that enables a diamond substrate with a large area to be manufactured in a short time and at a low cost.