The rest of his career was spent at Trinity College, where he was a Senior Fellow (1836–1852), Professor of Oratory (1816–1852) and an "efficient" Bursar (1836–1844), bringing the accounts of the collegiate estates into satisfactory order.

In 1852, George Villiers, 4th Earl of Clarendon, Lord-Lieutenant of Ireland, appointed him the 29th Provost of Trinity College Dublin, succeeding Franc Sadleir.

[3] MacDonnell was said to have had 'an excellent dry sense of humour', demonstrated on one occasion when showing a lady around the impressive Trinity College Library, Dublin.

On another occasion, after the plates had been cleared between the courses of a dinner he was hosting, his butler quietly placed a sugar cube on his bald head.

Still, after his mother died there the previous year, in 1837, he leased it out and bought a plot of land by the seafront at Dalkey, where he built a new country retreat, Sorrento Cottage, now owned by The Edge of the Irish rock band U2.

In the early 1840s, MacDonnell devised a plan for the construction of 22 houses right into the corner near the boundaries of the cottage, a huge undertaking at the time that was stalled almost immediately due to the Great Famine – the family having decided to help those around them rather than themselves.

The family stipulated that each house had to adhere strictly to the design of architects Frederick Darley and Nathaniel Montgomery.