The new church was designed by James Elliott of Chichester at a cost of £676 of which £309 was raised by private subscription. This included £80 from the Rev. George Curteis Luxmore, who was the curate of the absentee Rector in Middleton when the church was finally closed in 1837, and who became the first Rector of the new church –although he lived in Felpham. Other major contributors were the Church Building Society, the Chichester Diocesan Association, and the Coast Guard Office. This last is the clue to the decision to rebuild despite the tiny population, for the nineteenth century saw a sudden influx of people from the establishment of ten Coastguard Houses at Elmer, whose varying families added over 100 souls to the village. The new church was designed to seat 130 (110 free and 20 rented sittings)
The then new St Nicholas was dedicated on 23 April 1849. Its simple nave and narrow lancet windows are in a vaguely medieval style as though echoing the old church. Originally the East End finished square at the line of the sanctuary steps, with coloured glass in a triple lancet window above the altar; there was no entrance porch, no vestry and no provision for music. Across the back of the altar ran the inscription HOLY HOLY HOLY, and the Ten Commandments were painted on a plaque up on the East wall.