Under the control of the Kingdom of Ronda during the Moorish period, the town flourished as one of its principle fortresses, 17 kilometres south of the capital. Later, Alpandeire became the refuge of defeated Moorish ruler Hamet el Zegri. It was officially declared an independent village in 711AD.
After the Christian conquest in 1485, the Morisco population survived in two areas of population, the pueblo itself and the deserted village of Pospitar, both under the control of the Duke of Medina Sidonia. As elsewhere, the region was depopulated under expulsion orders from Felipe III and resettled by 22 new families from the north of Spain.
At the same time, the Bishop of Seville had ordered the construction of a church in 1505, of cathedral proportions dedicated to San Antonio de Padua. The pueblo honours his memory with a procession on 15 - 18 August each year.
Being such a large church, it hosted a visit by the Granada Tribunal of the inquisition in 1560 which netted a host of victims. Of the four who were found guilty, all were accused of continuing Moorish observances. Hernando Atafe and Juan Mayordomo were both fined for slaughtering animals using Moslem methods. Isabel de Madrid was also fined for adopting Moorish customs and dress. Her surname is of interest as many Moslems who converted to Christianity took the surname of the town that baptised them. Isabel may have come from central Spain, probably as a victim of a repopulation programme. Juan Moreno was convicted for the same "crimes" and imprisoned in Granada.
In 1815 the village was granted the award of Villazgo by Royal Privilege of Fernando VII for the pueblo's resistance during the French invasion.
The village is famed as the birthplace of a bearded monk, known later as Fray Leopold de Alpandeire. Born on 24 June 1866 and baptised as Francisco Tomas Marquez Sanchez, he became a local celebrity at the turn of the 19th century. At the age of 33 he left the village to become a Capuchin monk in Granada, where he remained until his death in 1956. His good work has attracted a number of miracles and his tomb is regularly visited by believers in search of divine help. The process of his beatification began in 1961 and sainthood may follow at some point. A monument to him can be found on the outskirts of the village, and following in his footsteps his birthplace in the village and a later home on the Ronda road can also be spotted.
The pueblo is not as isolated today as other local villages and the middle classes of Ronda have brought some prosperity to this community.