Muir arrived at Fort Victoria along with a party of miners and labourers from Scotland on the Harpooner on May 31, 1849 and departed aboard the Mary Dare for the coal deposits at Fort Rupert on August 28. Among the 'Muir Party' spending the summer at Fort Victoria were John's wife Annie and their four sons; Andrew, John, Michael, Robert; a nephew, Archibald Muir; John and Mary McGregor and John Smith. Roderick Finlayson put them to work at various tasks around the Fort for the three months of their stopover and, when they departed, Eden Colvile reported they “left this place very well satisfied”. However, labour disputes and conflict with the local indigenous population characterized Muir's years at Fort Rupert and when his contract expired in 1851 he settled briefly at Sooke before returning to serve the Company once again when coal was discovered at Nanaimo in 1852. Subsequently, he took over Walter Grant's farm at Sooke where the family settled in 1854. He went on to build a sawmill which produced lumber for export and become the area’s first representative in the House of Assembly for the Colony of Vancouver Island in 1856. He died at Sooke in 1883.