He wrote in his student journal notes that he was motivated to transfer his studies by the preaching of the pastor Johannes Hendricus Donner [nl], who was also ministering in Leiden by that time.

He studied under prominent faculties such as Johannes Scholten and Abraham Kuenen, and finally graduated in 1880 from the University of Leiden having completed a dissertation on the ethics of Ulrich Zwingli.

While serving there, he also assisted his denomination that had formed out of the withdrawal of orthodox Calvinists earlier from the state Hervormde Kerk, a withdrawal movement called the "Afscheiding" (Secession) in its merger with a second and subsequent larger breakaway movement that also left the Hervormde Kerk, this time under the leadership of Abraham Kuyper, a movement called the "Doleantie" (the Complaint: a historical reference to the term used by orthodox Reformed ministers who opposed Arminianism prior to the National Synod of Dordt, 1618–19).

Already, when the Afgescheidenen merged with the Dolerenden, there was a minority of the Seceders who stayed out of the union; they formed their new denomination as the Christelijke Gereformeerde Kerken (CGK), and they established their own theological seminary in the town of Apeldoorn.

Amidst all these developments, Bavinck stayed put and pursued his class lectures, research, writing, and publication – making his distinctive mark as an orthodox Calvinist theologian and churchman.

The recently founded Free University in Amsterdam (VU), under the leadership of Abraham Kuyper, was meant to be a bastion of Reformed learning in all fields of thought.

The Free University including its Theology Faculty for training clergy, unlike Kampen Seminary, was independent of both the state and all church denominations.

So, Bavinck, when he was first invited to join the VU Faculty, had to weigh the merits of teaching what concerned him in his theological research, in such a seemingly independent environment.

A comparison of the two positions, which came to designate two interwoven and contentious traditions in the GKiN and the neo-Calvinist Christian social movements that flowed from its membership, is presented in Jacob Klapwijk's important work of Reformational philosophy, entitled Bringing into Captivity Every Thought (English, 1986).

Other works have attempted to locate the center of Bavinck's thought in a grace-restores-nature structure: “...the essence of the Christian religion consists in the reality that the creation of the Father, ruined by sin, is restored in the death of the Son of God and the re-created by the grace of the Holy Spirit into a kingdom of God.”[18][19] Fundamentally, Bavinck's concern was to overcome philosophical dualisms by an assertion of a worldview distinctly Trinitarian, Reformed, and organic, and the fact of his life-long confessional standing as a minister within the Dutch Christian Reformed Church should not be overlooked.

Bavinck holds dogmatic theology to be a scientific exercise based on foundations of thought and reality.

[18] A dogmatic theologian, Bavinck was concerned with reordering categories of human thought in relation to God as first principle.

Bavinck was part of the movement known as Neo-Calvinism, and thus held to high views of theology proper and divine sovereignty as extending from the Calvinist tradition.

This knowledge does not arise from their own investigation and reflection, but is due to the fact that God on his part revealed himself to us in nature and history, in prophecy and miracle, by ordinary and by extraordinary means.

The fool may say in his heart, "There is no God," but those who open their eyes perceive from all directions the witness of his existence, of his eternal power and deity (Isa.

[18]In other words, for Bavinck, the idea of God's essence is thus tied to finite reality as revealing him, a nexus of ontology and epistemology.

"[18] Again echoing Calvin, Bavinck adopts language of accommodation to explain how God reveals himself to humanity, expanding the idea of accommodation to consider that all of creation, having been created to mirror God, is thus an anthropomorphism, including human speech about the divine: "…God, not the creature, is primary.

The possibility of his condescension cannot be denied since it is given with creation..."[18] Considering this view of the divine nature, Bavinck holds to classical high theological concepts surrounding the essence and attributes, holding to divine simplicity: "...God is 'simple,' that is, sublimely free from all composition, and that therefore one cannot make any real distinction between his being and his attributes.

The entire Reformed Dogmatics is structured on the Trinitarian formula of Father, Son, and Holy Spirit, with the exception of volume 1 as a prolegomena.