The church was rebuilt in 1603 by Rawlinson Greenhead, the year of his death. It was restored again in 1710-1711 and 1712 at a cost of £45-10- 9d. In 1721 the north transept was built, during this building work certain parties who objected to the transepts construction interfered with the work and were excommunicated and imprisoned in Lancaster Goal. The church was re-seated in pitch pine at a cost of £216-17-6d, these same seats serve the church very well to the present day.
After falling into disrepair the church was again restored in 1890 at a cost of £900, (including special gifts) and money was raised by public subscription, and two grants received from the Carlisle Diocesan and the church building society. This restoration involved removing the old Gallery from the West wall and the discovery under the floor of an ancient font which is now near the west door and used for christenings, new windows were placed in the chancel and north transept, replacing old wooden ones, modern heating apparatus was installed and a new pitch pine floor was installed.
In ancient times the dead were buried in Dalton and later in Hawkshead. Links with Hawkshead were severed in 1676 but burials still took place there. Colton church yard was enlarged in 1886 at a cost of £340 and the ground consecrated by the Lord Bishop the same year.
On the 7th of June 2003 a Concert and Dedication was held in the church to dedicate the new Jubilee window, each pane of glass in the three leaded windows was paid for by donations from parishioners.