Isles of Scilly on Wikipedia.

Listings are by island.
 

Bryher
There was a short-lived Baptist Chapel on the island from circa 1830 until at least 1843. The Baptist Home Ministry, which ran the chapel, withdrew from the island in 1843, though prayer meetings have continued without a minister for some time before the building was abandoned. Services were subsequently held (by a Methodist lay preacher) in a cottage at SV 87812 14753. © Carole Sage (2017). The need for a new Baptist Chapel eventually became apparent, and it was built in 1876-7. It was also used by the Bible Christians and Methodists. It's now a private residence. Another view. SV 87900 15014. Both © Carole Sage (2016).
All Saints (1742). SV 87991 14910. © Roy Graham. Another view, © Carole Sage (2006). Two additional views - 1, 2, two interiors - 1, 2, the pulpit, font (1861), and a window by Oriel Hicks (2007), all © Carole Sage (2016). Grade II listed.

St. Agnes
The former Bible Christian Chapel dates from the 1830's. Long closed, it became the island's Reading Room, and is now the island's Hall. The large extension is recent, and provides improved community facilities. Both © Carole Sage (2016).

St. Agnes of Rome, at Periglis, was built in the early 19th century to replace one of the 16th or 17th century (the second on the site), which fell victim to a storm. The money to re-build was raised through the sale of a wrecked ship, and the church bell also came from the ship. SV 87744 08296. © Roy Graham. Two additional views - 1, 2, the interior, pulpit and the font. The church has some charming modern stained glass, an example being this one, depicting boats heading out to sea on an errand of mercy. All © Carole Sage (2016 and 2018). Grade II listed.

St. Helen's
Now uninhabited, the island has the earliest known Christian site on the islands. According to archaeological investigations, St. Elidius' Hermitage consisted of a chapel and living cell (8th century), a small church of the 11th/12th century with associated graves, and 12th century living cells. The island isn't served by a boat service, so this distant view of the site was taken from another island. The site of the remains is on the pale patch of grass to the left of centre. SV 90091 16870. © Carole Sage (2016). The following photos from the excavations are all © Katharine Sawyer - 1, 2, 3, 4.

St. Martin's
Of the medieval chapel on Chapel Down, nothing survives other than the wall footings. Carole cautions that much on-line material claiming to show the chapel in fact show what remains of a nearby Napoleonic look-out station. Carole has had confirmation from local archaeologist Katharine Sawyer that her photos are actually of the chapel. Another view. SV 94204 16096. All © Carole Sage (2016).
Methodist Church at Higher Town. Dating from circa 1845, it was originally Bible Christian. SV 92913 15461. © Roy Graham. Another view (the lower part of the building is the church hall), and two interiors - 1, 2. all © Carole Sage (2016). Grade II listed.
St. Martin (1866). SV 92849 15618. © Roy Graham. Another view, two interiors - 1, 2, the altar, pulpit, font and a window (St. Martin giving half his cloak to a beggar). All © Carole Sage (2016). Grade II listed.

St. Mary's
A building in a terrace is currently a hair-dressing business, but was for a time used as a Baptist Chapel. Another view. SV 90469 10567. Both © Carole Sage (2017).
The former Bible Christian Chapel on Church Street in Hugh Town is now in use as a Masonic Hall. It was the first Bible Christian Chapel on the island - the congregation had previously met in a pub (see next entry). Its successor is now the islands Methodist Church (see below). SV 90469 10567. © Carole Sage (2016).
The Bishop and Wolf Inn was used in the 1820's by Bible Christian Missionaries from Cornwall to preach, prior to a purpose-built chapel being set up in Hugh Town (for which, see previous entry). © Carole Sage (2016).
The former Holy Vale Wesleyan Methodist Chapel. Built circa 1816, it's now in residential use. SV 91988 11630. © Carole Sage (2017). Carole has also found references to a Baptist Chapel at Holy Vale, but has been unable to establish any information other than its one-time existence. It doesn't appear to be marked on any old maps. Some sources also mention a monastery or convent having existed at Holy Vale at one time, but that seems to be erroneous.
Methodist Church on Church Street, Hugh Town, built as Bible Christian in 1899-1900. It became Methodist around the 1930's. Some of the fittings were transferred from the old Wesleyan Chapel in Hugh Town (see below). SV 90549 10561. © Roy Graham. Another view, and three interiors - 1, 2, 3, all © Carole Sage (2016). Grade II listed.
Our Lady Star of the Sea (R.C.) at Lower Strand, Hugh Town. Originally a girls' school (1860), the school transferred elsewhere, and the local catholic community leased it from 1931, later buying it outright. There is no longer a resident priest, services are held by the Penzance priest, with visiting priests during the summer. SV 90438 10558. © Roy Graham. Interior view, and a window, both © Carole Sage (2016).
St. Mary's, in Hugh Town dates from 1836-8. The vicar is accorded the title of Chaplain of the Isles, and is vicar for the whole island group. SV 90658 10584. © Roy Graham. Another view, the interior, window, and the font, all © Carole Sage (2016). A photo taken at dusk shows the illuminated cross which serves as a guide for boatmen returning to the harbour at night. © Carole Sage (2017). Grade II listed.
St. Mary in Old Town. Originally of the early C12, what remains today is, according to Pevsner, part of the original nave and side chapel (restored). SV 91112 10044. © Roy Graham. Four additional views - 1, 2, 3, 4, the interior, and the font. The former British Prime Minister Harold Wilson lies here. All © Carole Sage (2016, 2017 and 2018). Grade II* listed.
The site of the vanished chapel of St. Maudut is now occupied by the house gable-end on to the street at the bottom of the hill. Built around 1336, by the 18th century it was in use as a house, and it was demolished around 1830. Another view. SV 90152 10649. Both © Carole Sage (2008 and 2017).
The former Wesleyan Methodist Chapel on Garrison Lane, Hugh Town. It was the second on the site, the previous building dating from 1790. The building shown was succeeded by the Methodist on Church Street (see above), and it is currently used by the council as offices and council chamber, and as a Magistrate's Court. Two additional views - 1, 2. SV 90209 10539. All © Carole Sage (2017).
The former Wesleyan Meeting House at Old Town dates from the mid-19th century, and was the second on the site. There are references to the congregation using a dwelling-house before the chapel was built. It probably closed following the union of the Bible Christians and Methodists in the 1930's, when the former Bible Christian Chapel became the Methodist Church for the island (for which, see above). It was subsequently converted for residential use, and is now run as a B&B. SV 91486 10414. © Carole Sage (2016).

Samson
The island is no longer inhabited, the last people leaving in 1855. It never had a church, but one islander held prayers and bible readings in his now ruinous house, to which the other islanders were welcomed. © Katharine Sawyer.

Teän
Another now-uninhabited island, it once had a hermitage, known as St. Theona's Chapel. All that survives are some low walls. Another view. Both © Katharine Sawyer.

Tresco
The former Baptist Chapel, now a holiday cottage. It has also been a Reading Room and ad hoc doctor's surgery. SV 89038 15391. © Tresco Island/www.tresco.co.uk. Two additional views - 1, 2, both © Carole Sage (2018).
The remains of the Benedictine Priory, dedicated to St. Nicholas. Granted a charter in the 12th century, it's unusual in not having fallen victim to Henry VIII, but fell into disuse in the late 15th century, a victim of the depredations of pirates. Another view. SV 89451 14280. Both © Carole Sage (2018).
Non-conformism came relatively late to the island, as the Lord Proprietor wanted to encourage the population to attend the Anglican Church. However, two Methodist lay preachers used to hold prayer and worship meetings at their homes - shown here (SV 88987 15043; © Carole Sage (2017)) and here (SV 89177 15442; © Carole Sage (2009)). Eventually, a Wesleyan Chapel was built - at some date prior to 1829, when it is shown on a map. It appears however, that the hostility that accompanied the Methodists' arrival continued, and they were driven from the island "about 1847". It now serves as a school. Another view. SV 89310 15506. Both © Carole Sage (2017).
St. Nicholas (1878-9). It replaced two old cottages which stood on approximately the same site. These were used as a church by the SPCK. Locals conducted the services, with occasional visits by the chaplain from St. Mary's. There has been no resident vicar on the island since 1982. SV 89220 15419. © Roy Graham. Three additional views - 1, 2, 3, two interiors - 1, 2, the altar, pulpit, font, and a window, all © Carole Sage (2016 and 2018). Grade II listed.