Strata Florida was established in around 1164 by the Cambro-Norman Knight Robert FitzStephen (c. 1123—1183), the Monastery saw its origins in the 12th century. Cistercian monks from Whitland Abbey, Narberth, Carmarthenshire embarked on the construction of a new religious enclave along the banks of the Afon Fflur. This happened during a period of rapid expansion for the Cistercian order in England and Wales. The current Abbey derives its name from the Afon Fflur, and the original site of this early settlement is now referred to as Hen Fynachlog, translating to the Old Monastery.

Strata Florida evolved into a significant and influential religious hub. In approximately 1238, Prince Llywelyn ap Iorwerth convened a council at Strata Florida, where he secured the acknowledgment of his son Dafydd as the rightful heir by other Welsh leaders. The monastery exerted control over numerous farms, known as "granges," scattered across Wales, serving as essential sources of sustenance and revenue.

Notably, the monastery played a crucial role in the compilation of the Brut y Tywysogion, the most important primary historical source for early Welsh history. In 1401, during the initial stages of Owain Glyndwr's uprising, King Henry IV, along with his son, seized control of Strata Florida Abbey. The monks, perceived as sympathetic to Glyndŵr, were expelled from the monastery, which was subsequently looted. Henry IV repurposed the religious structures into a military stronghold with the intention of subduing any Welsh rebel forces in the vicinity. By 1402, the Earl of Worcester commanded the Abbey on behalf of the English Crown, maintaining a garrison comprising several hundred men-at-arms, archers, and foot soldiers. The site continued to serve as a military base for subsequent campaigns against Welsh rebels in 1407 and 1415. With the conclusion of the Glyndŵr rebellion, the monastic site was eventually restored to the Cistercians.