Combine plums, apples, and apple juice in a large pot over medium heat. Cover pot and simmer until tender, about 15 minutes. Mash fruit with a potato masher.
Stir agave nectar, cinnamon, cloves, nutmeg, and ginger into mashed fruit. Simmer, stirring frequently, until mixture thickens, 30 to 50 minutes. Cool completely, at least 1 hour. Pour apple butter into jars and cover with a lid; refrigerate for up to 3 weeks or freeze for up to 6 months.