In the Maltese archipelago, history and spirituality converge literally underground – in natural caves that have sheltered and inspired its inhabitants for millennia. These caves have been used for various purposes (shelter, burial and worship) from the early Neolithic, through pagan times, all the way into the Christian era. They alone provide visitors with a fascinating journey through Malta’s past –an expedition through sacred spaces in a palimpsest of cultures.
Perhaps most striking is how many of these caves have been transformed into Christian places of worship, including churches carved directly into the rock known as troglodytic churches – a true testament to Malta’s ancient religious traditions.
Neolithic beginnings: Għar Dalam and Temple Culture
Maltese use of caves as shelters and places of worship began with its first settlers, around 5900 BCE. These early inhabitants discovered in the island’s natural caves a source of physical protection and spiritual solace. Għar Dalam, one of Malta’s most famous prehistoric caves, contains evidence of human presence from this period, including tools and animal remains that paint a picture of Malta’s earliest days.

These caves probably served as sacred places for the Neolithic people who had already built the famous megalithic temples of Ħaġar Qim and Mnajdra. The caves, thought to be associated with fertility rituals and the worship of mother goddesses, represent Malta’s first known sites of spiritual importance. The act of retreating into the earth, of entering these subterranean spaces, probably had a symbolic meaning –perhaps evoking the idea of the womb or the underworld.
These early religious practices are a testament to the archipelago’s deep-rooted inclination towards religiosity and show how its very landscape invites and nurtures meditation. The rugged cliffs, vast stretches of coastline, and tranquil plains create a natural environment that seems designed contemplation. Indeed, the islands’ intimate scale encourages a sense of closeness to both nature and the divine. This unique interplay between place and spirit fosters a contemplative atmosphere that has drawn pilgrims and seekers throughout the centuries.
Pagan Worship and the Roman Era
Over the centuries, Malta’s caves witnessed the arrival of the Phoenicians and later the Romans, who brought their own religious practices, traditions, and gods to the islands. Some caves became places of pagan worship, often dedicated to fertility gods or chthonic deities. The Romans, for example, may have seen these caves as the dwellings of spirits or gods of the underworld, and they continued to use the grottoes for both practical and sacred purposes.
The Ħal Saflieni Hypogeum, although not a natural cave, reflects the same reverence for underground spaces. Used as a necropolis and ritual chamber, its carvings suggest that the Roman-Maltese continued to associate caves with spiritual practices even as they embraced new religious influences. It’s likely that several of these caves served as secret places for liturgical celebrations during the transitional period between pagan and Christian Malta.
The Christian Era and Troglodytic Churches
The history of Malta’s caves took a transformative turn in the year 60, when the Apostle Paul was shipwrecked on the island. According to the Acts of the Apostles, Paul spent three months on Malta, where he is believed to have taken refuge in a cave in Rabat. Today, St. Paul’s Grotto is a revered place of pilgrimage, marking the spot where Paul is said to have preached and spread Christianity on the island.

But St. Paul’s Grotto is just one of many Christian sanctuaries nestled in Malta’s caves. As Christianity spread throughout Malta, many caves were converted into Christian sanctuaries, even in the very early Middle ages. Indeed, plenty of early Maltese churches were built over ancient pagan temples (as was customary all throughout Christendom) to re-consecrate the site.
Since emperor Theodosius made Christianity the official religion of the empire after issuing the Edict of Thessalonica, Malta saw the development of troglodytic churches – places of worship carved directly into the rock. These underground chapels are evidence of the island’s deep Christian roots – as they were often used by early Christian communities seeking refuge from persecution.
One such example is the Chapel of St. Agatha in Rabat: an underground church that, according to tradition, served as a hiding place for Christians during periods of Roman persecution. Indeed, tradition claims Agatha herself lived here, as she fled from Sicily to Malta to escape persecution by the Roman Emperor Decius. The walls of St. Agatha’s Chapel are adorned with ancient frescoes preserved in the dim light of the cave – a treasure trove of early Christian art that offers a glimpse into the spiritual life of Malta’s early Christians.
St. Paul’s Grotto: A Sacred Legacy
Of all these grottoes, none is more famous than St. Paul’s Grotto in Rabat. According to tradition, this is the cave where St. Paul lived and preached during his stay in Malta. Today, it is a focal point for Christian pilgrims seeking to walk in the footsteps of the Apostle. The grotto is part of a larger religious complex that includes the Church of St. Paul and the Wignacourt Museum, making it a hub of Christian devotion.
A journey through time
Malta’s caves tell the story of an archipelago that has been a spiritual crossroads for thousands of years. Whether they sheltered Neolithic worshippers, Roman pagans or early Christian communities and saints, these caves bear witness to Malta’s evolving spiritual landscape. Some of these neolithic caves eventually developed into underground churches, and these churches into whole systems of catacombs –the most important ones outside of Rome. Today, many continue to serve as places of prayer and pilgrimage, offering travelers the chance to step into the sacred, timeless spaces that have shaped Malta’s history.
For those who explore the island’s caves, it is not just a matter of viewing geological wonders, but of experiencing a continuity of worship and devotion that stretches from the dawn of human settlement to the heart of Christianity. Whether standing in the prehistoric shadows of Ghar Dalam or kneeling in prayer at St. Paul’s Grotto, these sacred caves invite awe and a deeper understanding of the spiritual heritage that has shaped Malta (and the Mediterranean at large) for millennia.