An image pickup apparatus includes a processor configured of hardware functioning as a pixel-shift-combination processing section configured to perform pixel shift combination of a plurality of image data acquired by performing pixel shift photographing in a certain focus position to generate combined image data, a depth-combination processing section configured to perform depth combination of a plurality of combined image data in different focus positions that the depth-combination processing section causes the pixel-shift-combination processing section to generate, and a microcomputer configured to extract a focused region in at least one or more of the plurality of focus positions. The pixel-shift-combination processing section performs, concerning a focus position where the focused region is extracted, the pixel shift combination concerning only a partial image region including the focused region.