Around 1640 Jenkins revived the In Nomine, an archaic form for a consort of viols, based upon a traditional plainsong theme. He wrote a notable piece of programme music consisting of a pavane and galliard depicting the clash of opposing sides, the mourning for the dead and the celebration of victory after the siege of Newark (1646).

In the 1650s Jenkins became resident music-master of Lord Dudley North in Cambridgeshire, whose son Roger wrote his biography. It was in these years, during the Commonwealth under Oliver Cromwell, in the absence of much competition or organised music-making, that Jenkins took the occasion to write more than 70 suites for amateur household players.

He is noted for developing the viol consort fantasia, being influenced in the 1630s by an earlier generation of English composers including Alfonso Ferrabosco the younger, Thomas Lupo, John Coprario and Orlando Gibbons. Jenkins composed numerous 4, 5, and 6 part fantasias for viol consort, almans, courants and pavanes, and he breathed new life into the antiquated form of the In Nomine.