diff --git a/src/Apps/Apps.jl b/src/Apps/Apps.jl
index 2cf5b28fd1..0eba27043d 100644
--- a/src/Apps/Apps.jl
+++ b/src/Apps/Apps.jl
@@ -219,7 +219,8 @@ function add(pkg::PackageSpec)
     sourcepath = source_path(ctx.env.manifest_file, pkg)
     project = get_project(sourcepath)
     # TODO: Wrong if package itself has a sourcepath?
-    entry = PackageEntry(; apps = project.apps, name = pkg.name, version = project.version, tree_hash = pkg.tree_hash, path = pkg.path, repo = pkg.repo, uuid = pkg.uuid)
+    # PackageEntry requires version::Union{VersionNumber, Nothing}, but project.version can be VersionSpec
+    entry = PackageEntry(; apps = project.apps, name = pkg.name, version = project.version isa VersionNumber ? project.version : nothing, tree_hash = pkg.tree_hash, path = pkg.path, repo = pkg.repo, uuid = pkg.uuid)
     manifest.deps[pkg.uuid] = entry
 
     _resolve(manifest, pkg.name)
@@ -258,8 +259,8 @@ function develop(pkg::PackageSpec)
         pkg.repo.source = nothing
     end
 
-
-    entry = PackageEntry(; apps = project.apps, name = pkg.name, version = project.version, tree_hash = pkg.tree_hash, path = sourcepath, repo = pkg.repo, uuid = pkg.uuid)
+    # PackageEntry requires version::Union{VersionNumber, Nothing}, but project.version can be VersionSpec
+    entry = PackageEntry(; apps = project.apps, name = pkg.name, version = project.version isa VersionNumber ? project.version : nothing, tree_hash = pkg.tree_hash, path = sourcepath, repo = pkg.repo, uuid = pkg.uuid)
     manifest = ctx.env.manifest
     manifest.deps[pkg.uuid] = entry
 
diff --git a/src/Operations.jl b/src/Operations.jl
index 3cf9c77fe5..bf0c9b750f 100644
--- a/src/Operations.jl
+++ b/src/Operations.jl
@@ -345,7 +345,12 @@ function update_manifest!(env::EnvCache, pkgs::Vector{PackageSpec}, deps_map, ju
     # Build package entries
     for pkg in pkgs
         entry = PackageEntry(;
-            name = pkg.name, version = pkg.version, pinned = pkg.pinned,
+            name = pkg.name,
+            # PackageEntry requires version::Union{VersionNumber, Nothing}
+            # pkg.version may be a VersionSpec in some cases (e.g., when freeing a package)
+            # so we convert non-VersionNumber values to nothing
+            version = pkg.version isa VersionNumber ? pkg.version : nothing,
+            pinned = pkg.pinned,
             tree_hash = pkg.tree_hash, path = pkg.path, repo = pkg.repo, uuid = pkg.uuid
         )
         if is_stdlib(pkg.uuid, julia_version)