For a time the relationship of the new churches with the RCA was most cordial. At the invitation of the RCA through Dr. Wyckoff who visited the colony in 1849, the new arrivals formed themselves into Classis Holland of that denomination. This was completed in the spring of 1850 when Van Raalte attended the RCA synod meeting in Albany. Classis Holland then numbered 9 congregations. In those early years, Holland Academy was founded (1851), there was a decision of classis to undertake mission work to the "pagans," meaning their Native American neighbors (1852), and a declaration was issued against the institution of slavery (1855). The churches continued to grow steadily as new groups of immigrants arrived. Despite their poverty in this life on a new frontier, the groups were renowned by all who visited them for their spiritual fervor and warm devotion to the Scripture and Psalm-singing and for their care for one another. Several business ventures were launched, but most failed. The colonists were overwhelmed by the tasks just of clearing land, raising food and providing shelter for the continually arriving immigrants. It was a time of growth in isolation, with strong bonds formed by commonly shared adversity. The RCA continued to provide logistical and moral support.

Yet the new immigrants became increasingly uncomfortable with and suspicious of the eastern churches to which they had yoked themselves. Those churches were English-speaking (the new immigrants continued to use the "language of heaven," Dutch), hymn-singing (the new immigrants sang only Psalms), all too American-seeming (perfectly happy to use the state-operated schools for their children's instruction as opposed to schools which were more overtly and consistently Christian and Reformed) and had a great many Masonic Lodge members in their ranks and especially among their leaders (the immigrant groups saw such membership in secret societies as inconsistent with the profession of Christian faith). In hindsight it can be seen that Van Raalte's desire for peaceful relations and sense of gratitude towards the RCA folk who had done so much for the immigrants perhaps caused him to fail to approach the question of church affiliation carefully and deliberately enough. There was never any adequate examination of the RCA church order, no knowledge of its having altered the Canons of Dort (eliminating the "refutation of errors" sections) nor of its modification of the Belgic Confession, and there was simply a language barrier and, to some extent, cultural barrier, as well as the isolation of the new colony which hindered good communication.

The RCA Synod seemed to some of those delegated by the Michigan churches to an eastern synod to be lax in practicing closed communion and compromising in Reformed doctrine for the sake of ecumenicity. Some of those who spent some time in the East came to the colony and reported things like: no catechism preaching, administering the sacrament of infant baptism in home/family setting rather than in worship services, segregation of communicants by race, toleration of lodge membership, use of choirs and hymn-singing, interdenominational pulpit and table fellowship (the colony churches practiced strict closed communion), etc. The new immigrants objected to these things, and for some they made the maintenance of ecclesiastical bonds untenable. Several who had immigrated and settled in the East for awhile and moved later to the Michigan colony brought tales of the sorry state of the RCA in the East and inflamed feelings among those in the West.