The following year he arrived at Dunbrody, South Africa, with a team of about 30 monks from Maria Stern.  But due to drought and unsuitable land the mission was a failure.   On 20 December 1882 they travelled west of Durban to look at a farm.  The land was good, the Umhlatuzana river had fresh water and on 21 December they bought a part of the Zeekoegat Farm from the Land Colonization company.  There were discussions about what the new monastery would be called.  "Mary Ann Hill.  We will call it Mariannhill" declared the Prior.   ​In 1883 Father Francis returned from Europe with 34 new recruits.  After three years there were 150 monks and after ten years there were over 250 men.  They encouraged the local Shozi people to settle on the mission teaching them modern farming methods and establishing a monastery school for their children after the chiefs asked them to teach the children how to read 'the flies on the paper'.   In 1885 Mariannhill became an Abbey and Francis Pfanner was elected as the first Abbot of Mariannhill.  He knew that he would have to make changes to the customs of his order if they were to be effective missionaries so he advertised for nuns from Europe to join the Abbey as helpers.  In August, the arrival of the first five female mission helpers arrived from Europe.  They were the foundation of the new missionary Sisters of the Precious Blood and to this day they still serve in Mariannhill monasteries.  Any contact with women was forbidden by the Trappist order and the consequences were enormous.   In 1886 the Zulu Chief Sakayedwa in the Polela Valley near Underberg invited the monks to build schools within his community. The Abbot saw it as a challenge and purchased  land to set up a new mission.  It took the first nine monks fourteen days to get there from Mariannhill in six ox wagons which contained prefabricated living quarters manufactured at the Mariannhill Monastery to be used for accommodation, as well as food supplies, building materials and tools. In 1887 the mission was named Reichenau after a Benedictine monastery situated on the banks of Lake Constance in Germany.  In contravention of their order, the Trappists had become missionaries and evangelists. It soon became apparent that in order to spend every night under a Trappist roof in order to perform their seven hours of divine office, they would need to establish a network of mission stations each within a day's ride of each other.  In the next few years they established missions of Einsiedeln near Richmond (1887):  Oetting (1887): Mariathal near Ixopo (1887), Centocow near Donnybrook (1888), Kevelaer (1888) and Lourdes (1888) each with a unique church and a self-sustaining farm. But Abbot Pfanner's drive and ambition to change the lives of rural African people and the dispensations he gave to his monks, which went against many of their rules,  caused conflict within his beloved contemplative order and resulted in him being disposed as Abbot and banished to the far away mission of Emaus.  Here he hewed steps out of the rocks on the side of the mountain behind the mission, erecting a cross at the top which he called his Calvary.  He erected the Stations of the Cross on the way to the top and climbed the steps every day until, in his eighties, he could no longer walk.   His missionaries would not stop their missionary work or return to Europe. Eventually, in February 1909,  Pope Pius X decided to separate Mariannhill and all its missions from the Trappist order.  Those who wanted to stay with the order could go back to Europe but none returned.  A new order was created - the Congregation of the Missionaries of Mariannhill (CMM). Shortly after the creation of the CMM, on 24 May 1909, Francis Pfanner died at Emaus.  The stained glass window at Emaus installed in 1912 tells the story of Abbot Pfanner, the chiefs, the Sisters of the Precious Blood and other people who were a part of this amazing story.

Thomas Merton described the missionary work of Mariannhill:  'Here was the astonishing spectacle of a Trappist mission in which the contemplative monks had achieved in few short years, a success more spectacular than many active order had dared dream of. The most astounding thing about this new mission was that it was operating on purely Benedictine lines. It was an apostolate of prayer and labour (ORA ET LABORA), of liturgy and the plough. What was taking place in the outposts established by Dom Francis Pfanner was exactly the same process that had marked the Christianization of Germany and all northern Europe by the Benedictine monks hundreds of year before."