In 1232 construction was begun on a convent of the Order of the Cistercians under the name of Vallis Liliorum (St. Mary's Nunnery in the Valley of Lilies [de]), and the finished building was sanctified in 1264.

After the Reformation and the conversion of the Cistercian nuns, it became a Lutheran Women's Convent, and until the end of the Thirty Years' War in 1648 it remained in deplorable conditions.

After his early death in 1655, his wife Eleonora took over the government of the barony, with her seat in Osterholz, where she took an active role in the improvement of economic and sanitary conditions for the rural population.

Lilienthal remained a part of Swedish Bremen-Verden until 1712 (which is why the coat of arms contains the blue and yellow of the Swedish Flag), at which time it came under Danish occupation, and then in 1719 it fell under the sovereignty of the Electorate of Hanover, which ruled Bremen-Verden in personal union.

Due to the telescope, Lilienthal became well-known and was sought out in matters of astronomy by government and military officials.

The Befreiungskrieg (a series of battles fought between 1813 and 1815 that ended the Napoleonic Wars) hit Lilienthal hard.

In 1823 Bremen-Verden was united in a real union with the Kingdom of Hanover and its territory became part of the Stade Region.

Since 1 August 2014, public transport in Lilienthal has been upgraded by a line of Bremen Tramway, passing through its main street.