diff --git a/lib/mongoid/association/accessors.rb b/lib/mongoid/association/accessors.rb
index b4101b852e..aef9de5b46 100644
--- a/lib/mongoid/association/accessors.rb
+++ b/lib/mongoid/association/accessors.rb
@@ -251,6 +251,31 @@ def without_autobuild
         Threaded.exit_execution("without_autobuild")
       end
 
+      # Is the current code executing within an association setter?
+      #
+      # @example Is setter active?
+      #   document.in_setter?
+      #
+      # @return [ true | false ] If within a setter.
+      def in_setter?
+        Threaded.executing?(:in_setter)
+      end
+
+      # Yield to the block with setter flag enabled.
+      #
+      # @example Execute within setter context.
+      #   in_setter do
+      #     # setter logic
+      #   end
+      #
+      # @return [ Object ] The result of the yield.
+      def in_setter
+        Threaded.begin_execution("in_setter")
+        yield
+      ensure
+        Threaded.exit_execution("in_setter")
+      end
+
       # Parse out the attributes and the options from the args passed to a
       # build_ or create_ methods.
       #
@@ -345,15 +370,16 @@ def self.define_setter!(association)
         name = association.name
         association.inverse_class.tap do |klass|
           klass.re_define_method("#{name}=") do |object|
-            without_autobuild do
-              if value = get_relation(name, association, object)
-                if !value.respond_to?(:substitute)
-                  value = __build__(name, value, association) 
+            in_setter do
+              without_autobuild do
+                if value = get_relation(name, association, object)
+                  if !value.respond_to?(:substitute)
+                    value = __build__(name, value, association) 
+                  end
+                  set_relation(name, value.substitute(object.substitutable))
+                else
+                  __build__(name, object.substitutable, association)
                 end
-
-                set_relation(name, value.substitute(object.substitutable))
-              else
-                __build__(name, object.substitutable, association)
               end
             end
           end
diff --git a/lib/mongoid/association/embedded/embeds_many/proxy.rb b/lib/mongoid/association/embedded/embeds_many/proxy.rb
index f794aa3962..bba6d1b4b2 100644
--- a/lib/mongoid/association/embedded/embeds_many/proxy.rb
+++ b/lib/mongoid/association/embedded/embeds_many/proxy.rb
@@ -601,11 +601,31 @@ def as_attributes
           # @api private
           def update_attributes_hash
             if _target.empty?
-              _base.attributes.delete(_association.store_as)
+              handle_empty_target
             else
               _base.attributes.merge!(_association.store_as => _target.map(&:attributes))
             end
           end
+
+          # Check if we're currently in a setter
+          def in_setter?
+            _base.send(:in_setter?)
+          end
+
+          # Handle the case when the target is empty.
+          #
+          # @api private
+          def handle_empty_target
+            # Only persist empty array if:
+            # We're explicitly assigning (setter was called)
+            if _base.attributes.key?(_association.store_as) || in_setter?
+              _base.attributes.merge!(_association.store_as => _target.map(&:attributes))
+            else
+              # During initialization with no prior data, delete the key to maintain
+              # the original behavior of not persisting unassigned empty associations
+              _base.attributes.delete(_association.store_as)
+            end
+          end
         end
       end
     end
diff --git a/spec/mongoid/association/embedded/embeds_many/proxy_spec.rb b/spec/mongoid/association/embedded/embeds_many/proxy_spec.rb
index fa5471aeb7..35e7f7c2d6 100644
--- a/spec/mongoid/association/embedded/embeds_many/proxy_spec.rb
+++ b/spec/mongoid/association/embedded/embeds_many/proxy_spec.rb
@@ -4271,6 +4271,25 @@ class TrackingIdValidationHistory
     end
   end
 
+  context "when setting an embedded relation to an empty array" do
+    let(:document) do
+      Person.create!
+    end
+
+    let(:person) do
+      Person.find(document.id)
+    end
+
+    before do
+      person.update_attributes!(addresses: [])
+    end
+
+    it "sets the embedded relation to an empty array" do
+      expect(person.addresses).to be_empty
+      expect(person.attributes.keys).to include("addresses")
+    end
+  end
+
   context "when pushing with a before_add callback" do
 
     let(:artist) do
@@ -4771,18 +4790,38 @@ class DNS::Record
 
     context "in an embeds_many relation" do
 
-      let(:band) { Band.create! }
+      context "using .create! first" do
 
-      before do
-        band.labels = []
-        band.save!
+        let(:band) { Band.create! }
+
+        before do
+          band.labels = []
+          band.save!
+        end
+
+        let(:reloaded_band) { Band.collection.find(_id: band._id).first }
+
+        it "persists the empty list" do
+          expect(reloaded_band).to have_key(:labels)
+          expect(reloaded_band[:labels]).to eq []
+        end
       end
 
-      let(:reloaded_band) { Band.collection.find(_id: band._id).first }
+      context "using .new first" do
 
-      it "persists the empty list" do
-        expect(reloaded_band).to have_key(:labels)
-        expect(reloaded_band[:labels]).to eq []
+        let(:band) { Band.new }
+
+        before do
+          band.labels = []
+          band.save!
+        end
+
+        let(:reloaded_band) { Band.collection.find(_id: band._id).first }
+
+        it "persists the empty list" do
+          expect(reloaded_band).to have_key(:labels)
+          expect(reloaded_band[:labels]).to eq []
+        end
       end
     end
 
diff --git a/spec/mongoid/attributes_spec.rb b/spec/mongoid/attributes_spec.rb
index 1adc953561..76a4995363 100644
--- a/spec/mongoid/attributes_spec.rb
+++ b/spec/mongoid/attributes_spec.rb
@@ -2368,7 +2368,7 @@
         end
 
         it "updates the attributes" do
-          expect(doc.attributes).to_not have_key("pages")
+          expect(doc.pages).to be_empty
         end
 
         it "has the same attributes after reloading" do
@@ -2475,10 +2475,12 @@
         end
 
         it "updates the attributes" do
-          expect(doc.attributes).to_not have_key("pages")
+          expect(doc.pages).to be_empty
         end
 
         it "has the same attributes after reloading" do
+          puts doc.attributes
+          puts doc.reload.attributes
           expect(doc.attributes).to eq(doc.reload.attributes)
         end
       end
@@ -2495,7 +2497,7 @@
           end
 
           it "updates the attributes" do
-            expect(doc.attributes).to_not have_key("pages")
+            expect(doc.pages).to be_empty
           end
 
           it "has the same attributes after reloading" do