Most great English medieval churches were built of stone because stone was what wealthy parishes used. Hull built in brick. The choir of Hull Minster rose between roughly 1340 and 1370, the nave between 1380 and 1420, and the tower between 1490 and 1520, all in brick of remarkable quality. The transepts hold what architectural historians consider some of the finest medieval brickwork in England. The reason is geography. Hull sat on alluvial estuary clay with no good stone within easy reach, so the masons used the local clay to make bricks of unusual size and consistency, laying them in patterns that anticipate the great brick churches of the Hanseatic League across the North Sea. In the eighteenth century the brickwork was hidden under stucco, considered more refined; in 1842 to 1845 the architect Henry Francis Lockwood stripped it off again. The brick has been visible ever since.

In August 1759, a Hull merchant brought his infant son to Holy Trinity to be baptised. The baby was William Wilberforce, who would grow up in the city, serve as MP first for Hull and then for Yorkshire, and lead the parliamentary campaign that ended the British slave trade in 1807. The font where Wilberforce was baptised still stands inside the church. Hull, with its merchant fleets and its strong Methodist and Nonconformist traditions, was an unlikely cradle for the abolitionist movement; it was a port that had profited from the wider Atlantic trading economy of which slavery was part. But out of Hull came Wilberforce, and out of Holy Trinity came the man who would not let Parliament rest until the trade was ended. His statue stands today near the Minster, and the house where he was born is now a museum a short walk away.

Hull was the most heavily bombed city in Britain after London during the Second World War, easily found by Luftwaffe navigators following the line of the Humber Estuary from the North Sea. Whole districts of the city centre were levelled in raids during 1941. Holy Trinity stood within metres of streets that simply disappeared, but the church itself escaped serious damage. The miracle, if that is the word, allowed the medieval brickwork, the medieval stained glass that had been removed for safekeeping, and the tower with its clock dating from 1772 to survive into the second half of the twentieth century. The four clock dials installed by James Harrison in 1840 were, at the time, the largest parish church clock dials in England. The minute hand alone is over nine feet long.

The tower today holds two distinct sets of bells. A peal of twelve bells, ten cast in 1899 and two in 1959 by John Taylor of Loughborough, is used for traditional change ringing. A carillon of twenty-five smaller bells, installed in stages between 2013 and 2017, plays melodies controlled by a digital system or by a keyboard inside the tower. The organ is even more layered. The original 1711 instrument was built by Bernard 'Father' Smith from a 1704 organ that had proved too small for St Paul's Cathedral. John Snetzler enlarged it during the eighteenth century, Ryley of York rebuilt it in 1788, Forster and Andrews of Hull worked on it between 1845 and 1908, and the John Compton Organ Company expanded it into its present four-manual, 104-stop form in 1938. When the carillon and the organ and the bells all sound together on a feast day, the Minster reminds Hull that it is still listening.