With the closing of Ebenezer, Johannes was assigned as pastor of the German Church in Neu Hermannsburg. But, as noted in his first report in that capacity, he was also involved with the black congregation. "My work within the white congregation is as follows: every Wednesday morning from 8–9.30, I conduct a Church Service as well as Sunday school ... alternate Saturdays the evening devotion and Confession are led and Sundays the main Church Service. In addition, Confirmation Classes are conducted, funerals as well as visitations to the sick; baptisms and weddings ... amongst the blacks my duties are as follows: 4 days per week I conduct Religious Instruction in their school ... in the mornings from 9–10 including Catechism as well as Bible stories ... baptismal candidates are taught from 1–2, a time which is most unsuitable!" due to the heat of the day. As Missionary Hansen's health worsened, Johannes was called upon to do even more with the Zulu congregation. When Hansen died in March 1893, Johannes Lilje was left as the only ordained clergy in the area with responsibility for both Neu Hermannsburg congregations as well as several nearby mission stations. When Missionary Schulenburg was ordained, he took over the white congregation and Lilje took the black congregation. In 1890, Lilje was appointed to the Mission Advisory Board, where he served until his retirement.

During the 1890s, the German congregations of Natal were disrupted by the schism back home in Germany. Johannes frequently noted in his reports members leaving the congregation for fear of the Protestant "union" favored by Prussia. In 1893 many of the German congregations in Natal split, leaving fewer pastors to serve the people and the missions. Johannes notes: "The white congregation has held fast to God’s Word ... A few members have quarreled and scolded one another and had to be called to reconcile with one another. The unfortunate matter of separation has not yet raised its ugly head here, may God be praised for this!"

Among the black missions in the area, the issues were much closer to home. The Govern-ment's modernized marriage laws upset the natives. As Johannes points out in an 1894 report: "To give away their girls without getting 10 head of cattle will not be easily agreed to, it is such a convenient way to suddenly get rich." Another greed-based issue was of greater concern: "Of the men and young adults many are working in the goldfields, a place where temptations are huge, we do not know if they continue walking their path of faith loyally."

The bane of Johannes and the other missionaries were the evils of alcohol and prostitution particularly among their younger Zulu converts. In 1895 he wrote: "The condition of the black congregation remains unsatisfactory as indicated in the statistical report as 36 were removed. The absolute desire to excessive beer drinking is so strong that they fear no punishment and many have had to be turned away from Holy Communion; these bouts of drinking often include bloody beatings and so they also become guilty before the worldly law." In 1897 Johannes wrote: "Many persons, specifically the girls who are working in Greytown, committed the transgression of the 6th Commandment." and again in 1898: "Their immorality is enormous and whoring and unfaithfulness to their partners is bad.". In 1901 Johannes wrote: "Like little children they must be reminded time and again what they should or shouldn’t do."

Regarding the 2nd Boer War of 1899-1902, Johannes noted: "Hermannsburg has been spared by the war. Family and acquaintances in Transvaal, as well as our son,have been called up for active military duty by the government. We have not received any news of them. Whether our son is still alive or not, we do not know. We were saddened by the news that our Mission Director was taken captive." Certainly the shortages caused by the war impacted the people and their spiritual leaders, but the Lilje son and Mission Director were safe.

In the early years of the 20th century, concerns about pastoral salaries subsided, replaced by the unwillingness of younger Zulus to meet their church financial obligations. In 1904 Johannes wrote: "The young folk waste their money on worldly treasures and never have money for the church." Shortly before his retirement, in a 1905 report, Johannes states: "The actual duties of a missionary, to bring the Word of God to the heathens and to save them from Satan, are declining. Here we have to commit ourselves to reinforce God’s Word among the baptized." Times were changing. On January 10, 1906, Supt. Röttcher reported: "Brother Lilje asks to go on pension. He is old and has done great work in Hermannsburg. He retires in honour."

In 1907, the retired couple moved to son Wilhelm's farm in Müden, but this arrangement didn't last long. Johannes missed his life of service. They returned to Neu Hermmansburg where he conducted Sunday services for the German congregation and taught in the religious education program as a volunteer until he reached the age of 80. In July of 1914, Johannes officiated at the marriage of their youngest daughter, Maria Louise. They subsequently lived alone. In 1917 family, friends, and associates gathered to celebrate the 50th anniversary of Johannes' arrival in Natal. Click for Photo IDs and for family's certificate .

By early 1920, Johannes' ailments left the elderly couple unable to properly care for themselves. In May, they moved to Ehlanzeni where son-in-law Louis Reibeling was the missionary, hoping warmer weather and the ministrations of their daughter Auguste would help. It didn't. His obituary notes that even "here the old father became weaker by the day until he was bedridden a week before his death. At 10.00 in the evening on the 23rd September he silently and calmly passed away in the Lord." His wife lived on there for several years until Auguste's death in 1930. After that she lived with two of her sons in Schepersneck and Glückstadt until her own death in 1935. Her obituary notes that "She was a hard working, quiet, content and God-fearing person, she was loved and respected by all who knew her ... she had 8 [surviving] children, 57 grandchildren and 15 greatgrandchildren."