diff --git a/lib/mongoid/association/embedded/embeds_many/proxy.rb b/lib/mongoid/association/embedded/embeds_many/proxy.rb
index f794aa3962..90741f8602 100644
--- a/lib/mongoid/association/embedded/embeds_many/proxy.rb
+++ b/lib/mongoid/association/embedded/embeds_many/proxy.rb
@@ -601,7 +601,12 @@ def as_attributes
           # @api private
           def update_attributes_hash
             if _target.empty?
-              _base.attributes.delete(_association.store_as)
+              # Only remove the key if it is absent or nil. If it is already
+              # an empty array, the caller explicitly set it to [] (e.g. via
+              # a raw write_attribute call), and that intent must be preserved
+              # so the empty array is persisted to the database.
+              stored = _association.store_as
+              _base.attributes.delete(stored) unless _base.attributes[stored] == []
             else
               _base.attributes.merge!(_association.store_as => _target.map(&:attributes))
             end
diff --git a/spec/mongoid/association/embedded/embeds_many/proxy_spec.rb b/spec/mongoid/association/embedded/embeds_many/proxy_spec.rb
index 5b70621b8a..7f3386eb04 100644
--- a/spec/mongoid/association/embedded/embeds_many/proxy_spec.rb
+++ b/spec/mongoid/association/embedded/embeds_many/proxy_spec.rb
@@ -4524,6 +4524,39 @@ class DNS::Record
         expect(reloaded_band).not_to have_key(:labels)
       end
     end
+
+    context 'when set via raw attribute write in a before_save callback' do
+      after { Band.reset_callbacks(:save) }
+
+      let(:reloaded_band) { Band.collection.find(_id: band._id).first }
+
+      context 'on a new record' do
+        before { Band.before_save { self[:labels] ||= [] } }
+
+        let(:band) { Band.create! }
+
+        it 'persists the empty list' do
+          expect(reloaded_band).to have_key(:labels)
+          expect(reloaded_band[:labels]).to eq []
+        end
+      end
+
+      context 'on an existing record' do
+        # Reload the band from MongoDB so the labels proxy has not been
+        # initialized, which is the scenario that triggers the bug.
+        let(:band) { Band.find(Band.create!._id) }
+
+        before do
+          Band.before_save { self[:labels] ||= [] }
+          band.save!
+        end
+
+        it 'persists the empty list' do
+          expect(reloaded_band).to have_key(:labels)
+          expect(reloaded_band[:labels]).to eq []
+        end
+      end
+    end
   end
 
   context 'when using assign_attributes with an already populated array' do