The collapse of the Western Roman Empire in 476 AD led to a political authority disintegration and a brutal cultural decline. The Germanic tribes that dominated Western Europe after the collapse of the Western Roman Empire contributed very little to the evolution of pharmacy and medicine. The art of healing in Christianized Europe receded, returning to religious beliefs and folk medicine.

However, the inheritance of Rome and Byzantium was not totally lost in the Dark Age; in monasteries, monks were busy copying ancient manuscripts and preserving them. They knew the herbaria of the classical authors, such as Galen and Dioscorides, and applied their knowledge to the cultivation of medicinal plants such as sage, lavender, thyme, rosemary and valerian. In addition, many monasteries had pharmacies and hospitals where the practice of healing was developed. From the 12th century on several universities are founded throughout Europe under the domination of the Catholic Church, which reinforced the teaching of Hippocratic and Galenic medicine.

It is difficult to determine the exact moment when the apothecary appears in Western Europe. There were spice vendors, sellers of miracle powders, exotic medicinal drugs and spices at fairs and markets. Medieval doctors prescribed about a thousand natural substances, mostly of vegetable origin. There were also certain exotic substances that were said to have strange and special properties, such as the unicorn horn, the mandrake root and precious stones. Oriental spices, such as cloves, cinnamon or cardamom, enriched mixtures of essences composed of European herbs and aromatic flowers, like the lavender, tarragon, marjoram, oregano, thyme, basil and mint.

An important fact for the history of the Middle Ages pharmacy was the promulgation in 1240 by Frederick II, King of Sicily and Germanic Emperor, of the famous Magna Carta of Pharmacy, which separates pharmacy from medicine and legally recognizes the pharmaceutical profession.

Throughout the Middle Ages in Western Europe, classical medical knowledge was perpetuated and incorporated with the Arab contribution. Myth, magic and belief also played a key role in medieval medicine and pharmacy. However, despite all its involvement with the occult, the pharmacy in the Middle Ages achieved important victories: its separation from the medical profession; the recognition of the pharmaceutical profession; the physical establishment of the pharmacy; the emergence of professional pharmaceutical organizations; the introduction of pharmacopoeias into professional practice and the strengthening of the pharmacist's role as a public health agent.

At the end of the Middle Ages, Europe still witnesses the proliferation of rapid spread diseases, like plague, leprosy, scurvy, scabies, anthrax, lice outbreaks and various ophthalmic diseases, that have decimated its population.