Cuypers gave the architects working in his office considerable autonomy and Boeyinga, Johan van der Mey, Piet Kramer and Michel de Klerk, all of whom were more experimental than Cuypers himself, established the principle of what would later become known as the Amsterdam School, while working there.
During this period Boeyinga oversaw the construction of De Klerk's famous housing complexes at the Spaarndammerplantsoen in Amsterdam.
After the completion of his studies with a massive design for a government building in Amsterdam, the director of the municipal housing service, ir.
There was some controversy about the inclusion of statues at the entrance of Protestant leaders like Martin Luther, John Calvin and Kuyper.
In that period he became involved in the training of architects, first as a teacher, later as the head of a school for architecture in Amsterdam.