In 1900 it passed from the control of the founding Fathers of Mercy to the Congregation of the Blessed Sacrament, who introduced Eucharistic adoration as a worship style.

The center of the nave vault has trompe-l'œil paintings of the heavens; an elaborate Florentine-style floral pattern decorates the interior of the dome.

[5] Against the apse triforium on the east wall of the church stands the high altar with a mosaic half-dome, statues, and smaller bas-relief sculptures.

A. Letellier, rector, had a five-storey brick and stone rectory at 170–190 East 76th Street and 1067 Lexington Avenue built in 1911 to designs by Nicholas Serracino of 1170 Broadway for $80,000.

[7] From its origins in a rented hall above a stable[8] with an almost exclusively French Canadian congregation, St. Jean Baptiste has grown to be one of New York's most distinctive Catholic churches.

In 1841, Bishop de Forbin-Janson, on a missionary tour to the United States for the Fathers of Mercy, lamented that French-American Catholics in New York City had not been as devoted to raising churches in their national customs as Irish and Italian immigrants had.

A French Canadian immigrant community had begun to flourish in Yorkville at that time, and found it trying to make the trip downtown for services.

A missionary to this community found that services closer to home would be beneficial, similar to those the Jesuits at what is now St. Ignatius Loyola had organized for Yorkville's Germans.

The order's provincial gave his support for the establishment of a national parish, and a meeting of the immigrants' St. Jean Societé in 1881 raised $12 ($400 in contemporary dollars[10]) to that end.

Its projected cost was $20,000 ($654,000 in contemporary dollars[10]) but it soon ran into difficulties when problems with using the "crib of Bethlehem" forced the use of the unfinished church's basement during Lent in 1883.

A Canadian priest, Father J.C. Marquis, dropped in at the rectory unexpectedly on May 1, needing a place to stay while he carried a relic of the saint that Pope Leo XIII had given him back to Sainte-Anne-de-Beaupré, Quebec.

As a result, he was able to make a return trip to the shrine of St. Anne in Apt, France, and brought a relic back specifically for St. Jean Baptiste.

[9] In 1900 the efforts of a wealthy local Catholic activist, Eliza Lummis, brought the Congregation of the Blessed Sacrament (SSS), an international religious order of priests, brothers, and deacons founded by St. Peter Julian Eymard in Paris in 1856, to New York.

[9] The continuous exposure of the Sacrament, and the availability of daily confessions and early Mass at what was known as "Old St. Jean's" led to another increase in the size of the congregation.

[9] Ryan was initially skeptical of the dome, but when he saw how it won praise on a model of Serracino's design he authorized the additional $43,000 ($1.41 million in contemporary dollars[10]) for it.

The widening of Lexington Avenue also forced Serracino to scale back his original plans for a grand triumphal arch portico with full-width steps.

The lower church in the basement was finished and consecrated in 1913 by Camillus Paul Maes, bishop of the Roman Catholic Diocese of Covington, who had been the Congregation's strongest supporter in the U.S.

Early in the following year, he attended the first Mass celebrated in the upper church, even before the walls and ceilings were finished, by Father Letellier.

Cardinal John Murphy Farley, the archbishop, spoke at the end of the service and read a congratulatory telegram from Pope Pius X.

[12] Almost a year later, on November 29, 1919, Cecilia Simon, a maid at an East 56th Street home, was arrested in the church when she knocked statuary and a candelabra valued at $3,000 ($53,000 in contemporary dollars[10]) onto the floor and shattering them after a funeral service.

At services there the previous Sunday, investigators found that in a collection envelope she had placed a note registering her objection to the arrangement on the altar.

[13] In 1920 Mayor John Francis Hylan and Governor Al Smith were among the 100,000 Catholics who signed a petition to the new pope, Benedict XV, to designate St. Jean Baptiste a basilica.

[18] Work on the stained glass windows proved particularly challenging because the original installers had forced them into spaces too small for them, making them hard to remove.

It was necessary to hire more than the usual number of restorers, work overtime and locate the workshop in the dome rather than offsite in order to meet the church's fall 1997 deadlines.

[20] It was financed by the sale of land and air rights over a building formerly used as a convent by the sisters of Notre Dame, who subsequently moved into the upper floors of the rectory.

[21] It has been praised by a group of architects including Robert A.M. Stern for complementing the architecture of the adjacent rectory by echoing the church's bell towers and offering "rich sculptural form and lively surface patterning ... to a neighborhood burdened by so many uninspired blocklike apartment buildings"[22] In 2002, a longtime parishioner, Maryanne Macaluso, alleged that the new pastor, Father Mario Marzocchi, had groped and propositioned her after offering her a secretarial position.

After she complained to another priest and took paid leave due to the stress of having to see Father Mazocchi every day, the order had him evaluated by a psychologist who found nothing wrong with him, and then transferred him to a parish in Florida.

When she asked the replacement pastor, Father Anthony Schueller, for full-time work, he informed her that the church could not afford to do so and she requested a letter of termination, putting her in danger of being evicted from her apartment.

[23] After the state denied her unemployment claim on the grounds that she had left work voluntarily, Macaluso filed suit against the church, the order, the Archdiocese of New York, Cardinal Edward Egan, and Father Marzocchi.

[27] In the broader community, the church, in conjunction with the sisters of Notre Dame, continues to operate St. Jean Baptiste High School for girls.