In 1872, he entered into partnership with William J. McPherson (1821–1900), a leading decorative painter and interior designer, for whom he organized a stained glass department within the firm of W.J.
As early as 1872, he introduced "doubling" or layering glass for decorative and pictorial effect in a memorial window depicting "Charity and Devotion" at St. Anne's Episcopal Church in Lowell, Massachusetts.
At the direction of Ware and McPherson, he collaborated with John La Farge (1835–1910) on a number of experimental works and in 1874 produced the first opalescent picture window for Harvard's Memorial Hall (now lost).
Initially favoring English glass imported from Hartley of Sunderland and Powell of London, MacDonald was dedicated to the vitreous properties of his medium rather than painterly or illusionistic effect.
In an interview by local glass manufacturer Thomas Gaffield (1825–1900), when questioned about the awkward interior lighting effects sometimes created by a decorative window, he stated that he tried "to induce people to let the glass remain in its full beauty, undimmed by any enamel and if the sun troubled them to place curtains in the window and to pull them down until the light ceased to trouble them."
MacDonald's abilities as a collaborator along with his skill and sensitivity as an artisan appealed to rational thinking and liberal minded architects and designers.