As time went on, an increasing demand for accommodation in the school resulted in a roll of over 1,000 pupils by the late 1880s but thereafter, subsequent to the abolition of fees in public schools within the burgh and its immediate neighbourhood, the numbers fell. It was around this time also that the John Neilson Institution came under the control of the Paisley Educational Trust. Nevertheless, both in times of light and heavy rolls, the standards of the school were always maintained and it is significant that this was the only Scottish school to win a Gold Medal in the Paris Exhibition of 1900. It was in this year also that Departmental demands 'coincident with a diminishing income created extreme difficulties for the Directors of the school, from which they were rescued by the generosity of the Trustees of Wm. B. Barbour and Peter Brough. The infant school was then remodelled and equipment supplied to bring the school up to the standards required of the day to provide education as an "Intermediate " Higher Grade school which provided education for secondary pupils to the end of the third year only. Those pupils of the John Neilson Institution who wished to continue their day school education beyond that stage then proceeded to other schools in the area and there were not a few citizens of Paisley who as a result were former pupils of both the John Neilson Institution and of Paisley Grammar School.

In 1918 the school was transferred to the newly created Renfrewshire Education Authority and, at this time, those responsible for its well-being expressed considerable fears for the continuance of the tradition, ideals and independence of the school. But in 1918 a very liberal agreement was reached during the then transitional period and the fears of the traditionalists at that time have since proved completely groundless. Indeed, it was not many years after the responsibility for the school was transferred to the Education Authority that it grew to its former stature as a full secondary school offering its pupils courses continuing to the point of presentation for the Higher Leaving Certificate.