The architect Auguste Van Assche favoured a rather dogmatic approach, and wanted to restore the church to the original gothic style, one of the implications being that the 17th century western portal would have to be rebuilt. Preliminary works started at the beginning of the 20th century. The houses at the western and southern wings were demolished, but at the request of the archaeologist-draughtsman Armand Heins those at the northern side of the church were preserved. In 1906 architect H. Geirnaert advocated restoring the present situation instead of a historic reconstruction. But the plans were mothballed due to the First World War.

When the building was put on the preservation list on the 28th of December in 1936 new opportunities were created. The non profit organisation "De Vrienden van de St Niklaaskerk" was founded in the same year and has had as its main objective to stimulate the complete restoration of the church. Restoration works of the western wing, which had been knocked down in 1914, started again in 1938 and were completed in 1946. The result however, was severely criticised for a lack of fantasy.

Janssens died in 1953 and was succeeded by Adrien Bressers who submitted a new design for the restoration at a meeting of the representatives of the city, province and the Royal Commission on October 30 in 1957. They had seen the decay with their own eyes from the scaffold and were convinced of the necessity of a solid restoration based on an archaeological study of the site. So the principle not to change anything was abandoned. This paved the way for a study of testimonies and indications allowing a return to the original state. Prof. dr Firmin De Smidt started with archaeological research in 1960. The investigation of the stability was entrusted to Prof. Ir. F. Riessauw.