Heinrich Karl Gustav Hugendubel bought an existing bookshop at Salvatorplatz in Munich in 1893, laying the foundation for a German limited partnership, GmbH & Co. KG.

After Paul's death in 1943, his wife, Anneliese Hugendubel, assumed control, acting as managing chief until 1964 when their son, Heinrich Hugendubel, opened the first branch in Munich.

In January 2011, the company was accused of censoring its own trade union blog.

In cooperation with Weltbild publishing house, a "filter" was briefly applied to Hugendubel's online shop, which filtered out numerous gay and lesbian, church-critical, esoteric and communist articles.

After a unanimous critical media response, the filter was removed and titles were relisted.