A spokesman for the charities said the move was completed on 1 April and resulted in Arc Light becoming a subsidiary of Changing Lives while retaining its own branding and identity.
Arc Light, which has an income of £1.2m a year and 32 staff, is based in York and runs a 35-bed accommodation and support facility for homeless people in the city.
Changing Lives, formerly called Cyrenians, is based in Gateshead and provides support services for vulnerable people, including an addiction facility in York. It has a yearly income of £15.2m and 329 staff.
Eileen Ronan, a director at Changing Lives, will take charge of the charities’ operations in York when Jeremy Jones, who has been the chief executive of Arc Light for the past 17 years, retires at the end of May, the spokesman said.
There are no other job losses, and both charities’ York facilities will remain, he said.
Stephen Bell, chief executive of Changing Lives, said: "The merger makes perfect sense for all concerned. I have long been an admirer of the work that Jeremy and Arc Light have been doing and I’m delighted that they are joining the Changing Lives family.
"We have successfully merged with several charities in the past few years and working with the homeless has always been at our core."
Dean Fielding, chair of Arc Light and who has also joined the Changing Lives board, said: "These are difficult times for small charities. Changing Lives bring an understanding of Arc Light and a business that will help develop new income streams and support the expansion of the brand in York.
"We are all sorry to see Jeremy go, because he has been inspiration behind what Arc Light is today. And we welcome Eileen Ronan, who brings a number of complementary and additional skills, not least in the area of health and addictions."
Jones said: "I am very proud of all that we have achieved in York over the last 17 years and the recognition of Arc Light as a key provider of homeless services in the city.
"In Changing Lives, we have secured a fantastic partner to support our future growth and development."