The organ for Jesus College Chapel, built by William Drake in 1993 and refurbished by the Drake Workshop in 2016, has been conceived in the style of English instruments of the early nineteenth century. Organs of this period did not differ greatly from their eighteenth-century precursors, themselves little changed from post-restoration models which had been influenced by French and Dutch builders.

The sound of this organ reflects the move, which took place during this period, towards a broader and more mellow timbre coupled with greater dynamic range, which did not, however, obscure the colourful range of individual sounds which characterise older English instruments. At around the same time, pedals were introduced to control the lowest notes (they had already been in use for at least three centuries in mainland Europe), and the Swell organ, hitherto a treble section used to provide solo voices, was extended in the bass to encompass the same number of notes as the main (Great) keyboard. Both these developments are reflected in the new instrument, which is therefore not only suited for the performance of English music of the eighteenth and early nineteenth centuries, but also for the vast source of European organ music written before this date. The variety of soft sounds which may be obtained also makes it ideal for the accompaniment of choirs, solo voices and instruments.

The organ contains 1,792 pipes, each voiced in the chapel to suit the intimate acoustic and to blend with its neighbours. The pipes take various forms; most are made of a tin/lead alloy and are similar in shape to the pipes in the facade. Others are closed at the top, and some of the larger pipes are rectangular in section and made of pine. The pipes are grouped into stops, with one or more pipes for each note. The stops speak at various pitches relative to one another, thus allowing the organist to vary the brilliance of the timbre.

The pipes are grouped into three distinct departments: the Great organ is the principal division, containing most of the bolder stops, and is played from the lower keyboard; and the Swell organ is placed above the pipes of the Great organ; its pipes are enclosed in a box, the front of which is made up of moveable shutters. The Pedal organ stands behind in a separate case.

The organ is tuned to an unequal temperament (i.e. the intervals of the scale are not all the same size); this is based on historic English models, and gives each key its own distinct colour whilst not restricting the organist to a few "good" keys.

Wind is provided by an electric fan and fed to a wedge-shaped reservoir which serves to regulate the pressure. Within each department, all the pipes for one note stand over a common channel or "groove" into which air is admitted by means of a sprung valve, called a pallet. Each pallet is connected to the appropriate key by a series of mechanical linkages. The pipes are arranged in rows stop by stop; a thin strip of wood or "slider" runs longitudinally under each row, and is connected to a stop-knob. When a stop is drawn, holes in the slider line up with the feet of the pipes above, permitting air from the grooves to enter. The stops may be combined in any permutation as desired.

The main case, which is made of quarter-sawn English oak, stained and polished on site, is in a typical English form. The carvings include details from the late seventeenth-century screen below the organ; a closer look will also reveal two drakes' heads above the large central pipes. The case pipes, most of which speak, are decorated with gold leaf.

The materials and constructional techniques used in the instrument adhere faithfully to the historical concept outlined above; although machine tools have been used, virtually every component has been individually hand-finished. The organ took eighteen months to construct, four of which were spent in the chapel.