Political rivalry caused the removal of the Government Land Office from Doniphan to Kickapoo in 1859, which saw the beginning of the decline of the town. However, glowing reports still resounded regarding the town. In James Redpath’s Handbook to Kansas Territory, published in 1859, he presented an optimistic view, stating:
“Doniphan, it is admitted by everyone, has the best rock-bound landing, and the best townsite on the Missouri River anywhere above St. Louis. It has running through it, a fine stream of water, which by a trifling outlay which will soon be expended, can be made to flow through five of the principal streets. A wealthy company has been chartered for the construction of a railroad for St. Joseph, through Doniphan, for Topeka, connecting the Kansas and Missouri Rivers. The stock is subscribed — ten percent paid in. That part of it from St. Joseph to Doniphan will be completed as soon as the connection is made with Hannibal. Lots can be purchased at Doniphan on more liberal terms than at any other town on the Missouri. We say to the emigrant, come to Doniphan; believing as we do, that it is destined to be the great emporium of the upper Missouri. The population is about one thousand.”
In 1859, James H. Lane moved to Leavenworth and later that year, in December, aspiring presidential candidate Abraham Lincoln believed Doniphan to be important enough to visit. There, he spoke to the townspeople and stayed in the area for eight days campaigning. During this year, Forman’s Flouring Mill was destroyed by fire and a new mill of about the same capacity was at once erected and put in operation.
In 1860, the St. Charles Hotel, built in 1857, was destroyed by fire and the next year, when the Civil War began, Doniphan’s population declined sharply. The same year, the Doniphan Post newspaper began but lasted only about one year.
In 1861, Forman’s Flouring Mill burned again and afterward, James Forman retired from this branch of business and it was never rebuilt.
Doniphan’s population recovered after the Civil War and several brick buildings were erected, including a large warehouse. In 1865, the Catholic Church and residence burned down and two years later the new St. John the Baptist Catholic Church was constructed from brick on land donated by Adam Brenner, who was known for his expansive vineyards and wine operation. The new brick structure measured 26 x 50 feet and included a stately bell tower with a fine-toned bell weighing nearly half a ton. A cross gable wing measuring 24×36 was added around 1868. The church never had a residing full-time priest but was provided visiting priests from the Benedictine Abbey in Atchison. Today, the brick church is one of few significant structures that remain standing in Doniphan.
In 1867, Adam Brenner built an elevator with a capacity of 40,000 bushels, at a cost of $16,000. In the fall of 1868, the Doniphan House Hotel, after many changes of proprietors, was burned to the ground.
In 1869, George Brenner planted the first five acres of the famous Belleview vineyard. The same year, he erected a large two-story brick building to accommodate his wine interests. The building measured 65×44 feet, with a large cellar, and a storage room for 90,000 gallons of wine. The Brenner vineyards would eventually grow to occupy over 50 acres, employ dozens of workers for every harvest as well as year-round staff. The wineries produced as much as 150,000 gallons in their peak years, shipping to buyers all over the country.
The same year, Doniphan was incorporated, judges were appointed, and a city council was organized.
With the arrival of the railroad in northeast Kansas in 1870, the importance of the steamboat diminished and the advantages of Doniphan’s excellent steamboat landing began to fade. The Atchison & Nebraska Railroad arrived at Doniphan in January 1871. At that time, there were 228 families in Doniphan, with a population of 1,020. That year, the Doniphan Democrat newspaper was launched in May and ran for about a year. Afterward, it was taken over by new owners and published briefly as Doniphan Herald in the summer of 1872, and then discontinued.
In 1872, a fire burned Adam Brenner’s large grain elevator, along with its contents, a large amount of grain. However, the vineyards were still doing well, as attested to by the Doniphan Herald, which stated:
“We visited the wine cellars of the Brenners this week, and to say that we enjoyed the sparkling fluid from the 1,000-gallon cask, would not half express our delight in that visit. Such delicious wines are not found elsewhere in the United States. Those Brenner wines are getting a reputation not to be excelled anywhere in the country. Hermann [Missouri] has heretofore claimed the laurel in wines, but Doniphan now so far surpasses her in quality that Hermann must stand aside.”