Provided are an imaging unit, an endoscope, and a method of manufacturing an imaging unit for preventing breakage of a multi-layer substrate while achieving a reduction in size. The imaging unit according to the present invention includes: a solid state image sensor a flexible substrate extending to a surface side opposite to a light receiving surface of the solid state image sensor and a multi-layer substrate connected to a surface of the flexible substrate, the surface of the flexible substrate being a surface to which the solid state image sensor is connected, the multi-layer substrate including a plurality of electronic components mounted thereon. The multi-layer substrate includes, on a proximal end side relative to a connection portion between the flexible substrate and the multi-layer substrate on a connection surface to which the flexible substrate is connected, a recessed portion in which at least one of the electronic components is mounted. The depth of the recessed portion from the connection surface is less than the height of the at least one of the electronic components mounted in the recessed portion. The at least one of the electronic components mounted in the recessed portion is configured not to project from a surface of the flexible substrate opposite to a connection surface of the flexible substrate, the connection surface of the flexible substrate being a surface to which the multi-layer substrate is connected.
