diff --git a/lib/bundler/multilock.rb b/lib/bundler/multilock.rb
index f38f11d..c3a5ce5 100644
--- a/lib/bundler/multilock.rb
+++ b/lib/bundler/multilock.rb
@@ -167,7 +167,7 @@ def after_install_all(install: true)
             up_to_date = false
             Bundler.settings.temporary(frozen: true) do
               Bundler.ui.silence do
-                up_to_date = checker.base_check(lockfile_definition) &&
+                up_to_date = checker.base_check(lockfile_definition, check_missing_deps: true) &&
                              checker.check(lockfile_definition)
               end
             end
diff --git a/lib/bundler/multilock/check.rb b/lib/bundler/multilock/check.rb
index 4b7a87b..662f381 100644
--- a/lib/bundler/multilock/check.rb
+++ b/lib/bundler/multilock/check.rb
@@ -58,7 +58,7 @@ def run(skip_base_checks: false)
 
       # this is mostly equivalent to the built in checks in `bundle check`, but even
       # more conservative, and returns false instead of exiting on failure
-      def base_check(lockfile_definition, log_missing: false, return_missing: false)
+      def base_check(lockfile_definition, log_missing: false, return_missing: false, check_missing_deps: false)
         return return_missing ? [] : false unless lockfile_definition[:lockfile].file?
 
         Multilock.prepare_block = lockfile_definition[:prepare]
@@ -83,7 +83,10 @@ def base_check(lockfile_definition, log_missing: false, return_missing: false)
 
         return not_installed if return_missing
 
-        not_installed.empty? && definition.no_resolve_needed?
+        return false unless not_installed.empty? && definition.no_resolve_needed?
+        return true unless check_missing_deps
+
+        (definition.locked_gems.dependencies.values - definition.dependencies).empty?
       ensure
         Multilock.prepare_block = nil
       end
diff --git a/spec/bundler/multilock_spec.rb b/spec/bundler/multilock_spec.rb
index 872b5c0..5013b67 100644
--- a/spec/bundler/multilock_spec.rb
+++ b/spec/bundler/multilock_spec.rb
@@ -716,6 +716,26 @@
     end
   end
 
+  it "removes now-missing explicit dependencies from secondary lockfiles" do
+    with_gemfile(<<~RUBY) do
+      gem "inst-jobs", "3.1.13"
+      gem "activerecord-pg-extensions"
+
+      lockfile("alt") {}
+    RUBY
+      invoke_bundler("install")
+
+      write_gemfile(<<~RUBY)
+        gem "inst-jobs", "3.1.13"
+
+        lockfile("alt") {}
+      RUBY
+
+      invoke_bundler("install")
+      expect(File.read("Gemfile.lock")).to eq File.read("Gemfile.alt.lock")
+    end
+  end
+
   private
 
   def create_local_gem(name, content = "", subdirectory: true)