The two organisations, which announced in January that they were considering a merger, said they had agreed to proceed.
Lincolnshire YMCA has 76 employees and had an income of £2.3m in 2011/12. The Nomad Trust had an income of £570,000 in 2011/12 and has 16 staff. The names and branding currently used by the two charities will be retained.
Malcolm Barham, chief executive of Lincolnshire YMCA, will lead the new organisation. No other decisions on staffing have been made.
Barham told Third Sector: "There will be no changes in staffing for at least three months – everybody will transfer to us and once we are one organisation together we will review the services we offer as a group.
"Thanks to the merger we will have every service we need to help people on their journey from homelessness and sleeping rough to independent living and accommodation. Since we announced the merger talks, we’ve already had contact from three local authorities to discuss the possibility of providing services for them."
A top priority for the new charity is to find a site for a new shelter for homeless people in Lincoln, Barham said. This is intended to be opened in two years time, with up to 30 bed spaces, and staff will remain in their current locations until the new facility is ready.