diff --git a/lib/stroma/dsl/generator.rb b/lib/stroma/dsl/generator.rb
index 8bfa489..4ce23bb 100644
--- a/lib/stroma/dsl/generator.rb
+++ b/lib/stroma/dsl/generator.rb
@@ -16,6 +16,19 @@ module DSL
     # - ServiceClass gets @stroma_matrix (same reference)
     # - ServiceClass gets @stroma (unique State per class)
     #
+    # ## Deferred Entry Inclusion
+    #
+    # Entry extensions are NOT included via `Module#include` at the base class level.
+    # Instead, only the `self.included` callback is fired (via `send(:included, base)`)
+    # to set up ClassMethods, constants, etc. The actual module insertion into the
+    # ancestor chain (`append_features`) is deferred until {Hooks::Applier} interleaves
+    # entries with hooks in child classes.
+    #
+    # **Contract:** Entry extensions MUST implement `self.included` as idempotent.
+    # The callback fires twice per entry per class hierarchy:
+    # 1. At base class creation (deferred, via `send(:included, base)`)
+    # 2. At child class creation (real, via `include` in {Hooks::Applier})
+    #
     # ## Usage
     #
     # ```ruby
@@ -75,7 +88,13 @@ def included(base)
               base.instance_variable_set(:@stroma_matrix, mtx)
               base.instance_variable_set(:@stroma, State.new)
 
-              mtx.entries.each { |entry| base.include(entry.extension) }
+              # Deferred inclusion: triggers `included` callback without `append_features`.
+              # The callback runs ClassMethods/Workspace setup on base.
+              # `append_features` (actual module insertion into ancestors) is deferred
+              # until Applier interleaves entries with hooks in child classes.
+              # NOTE: `included` will fire again when Applier calls `include` on child,
+              # so entry extensions must design `self.included` as idempotent.
+              mtx.entries.each { |entry| entry.extension.send(:included, base) }
             end
           end
 
diff --git a/lib/stroma/hooks/applier.rb b/lib/stroma/hooks/applier.rb
index 33e3418..2c83992 100644
--- a/lib/stroma/hooks/applier.rb
+++ b/lib/stroma/hooks/applier.rb
@@ -2,13 +2,15 @@
 
 module Stroma
   module Hooks
-    # Applies registered hooks to a target class.
+    # Applies registered hooks to a target class with deferred entry inclusion.
     #
     # ## Purpose
     #
-    # Includes hook extension modules into target class.
-    # Maintains order based on matrix registry entries.
-    # For each entry: before hooks first, then after hooks.
+    # Manages hook and entry module inclusion into the target class.
+    # Operates in three modes depending on current state:
+    # - No hooks: returns immediately (entries stay deferred)
+    # - Entries already in ancestors: includes only new hooks
+    # - Entries not in ancestors: interleaves entries with hooks for correct MRO
     #
     # ## Usage
     #
@@ -50,16 +52,59 @@ def initialize(target_class, hooks, matrix)
 
       # Applies all registered hooks to the target class.
       #
-      # For each registry entry, includes before hooks first,
-      # then after hooks. Does nothing if hooks collection is empty.
+      # Three modes based on current state:
+      # - No hooks: return immediately (defer entry inclusion)
+      # - Entries already in ancestors: include only hooks
+      # - Entries not in ancestors: interleave entries with hooks
       #
       # @return [void]
       def apply!
         return if @hooks.empty?
 
+        if entries_in_ancestors?
+          include_hooks_only
+        else
+          include_entries_with_hooks
+        end
+      end
+
+      private
+
+      # Checks whether all entry extensions are already in the target class ancestors.
+      #
+      # Uses all? so that partial inclusion (some entries present, some not)
+      # falls through to include_entries_with_hooks where Ruby skips
+      # already-included modules (idempotent) and interleaves the rest.
+      #
+      # @return [Boolean]
+      def entries_in_ancestors?
+        ancestors = @target_class.ancestors
+        @matrix.entries.all? { |e| ancestors.include?(e.extension) }
+      end
+
+      # Includes entries interleaved with their hooks.
+      #
+      # For each entry: after hooks first (reversed), then entry, then before hooks (reversed).
+      # reverse_each ensures first registered = outermost in MRO.
+      #
+      # @return [void]
+      def include_entries_with_hooks
+        @matrix.entries.each do |entry|
+          @hooks.after(entry.key).reverse_each { |hook| @target_class.include(hook.extension) }
+          @target_class.include(entry.extension)
+          @hooks.before(entry.key).reverse_each { |hook| @target_class.include(hook.extension) }
+        end
+      end
+
+      # Includes only hook extensions without entries.
+      #
+      # Used when entries are already in ancestors (multi-level inheritance).
+      #
+      # @return [void]
+      def include_hooks_only
         @matrix.entries.each do |entry|
-          @hooks.before(entry.key).each { |hook| @target_class.include(hook.extension) }
-          @hooks.after(entry.key).each { |hook| @target_class.include(hook.extension) }
+          @hooks.before(entry.key).reverse_each { |hook| @target_class.include(hook.extension) }
+          @hooks.after(entry.key).reverse_each { |hook| @target_class.include(hook.extension) }
         end
       end
     end
diff --git a/sig/lib/stroma/hooks/applier.rbs b/sig/lib/stroma/hooks/applier.rbs
index 628e090..e9ca196 100644
--- a/sig/lib/stroma/hooks/applier.rbs
+++ b/sig/lib/stroma/hooks/applier.rbs
@@ -10,6 +10,14 @@ module Stroma
       def initialize: (Class target_class, Collection hooks, Matrix matrix) -> void
 
       def apply!: () -> void
+
+      private
+
+      def entries_in_ancestors?: () -> bool
+
+      def include_entries_with_hooks: () -> void
+
+      def include_hooks_only: () -> void
     end
   end
 end
diff --git a/spec/stroma/dsl/generator_spec.rb b/spec/stroma/dsl/generator_spec.rb
index c2f5b2c..4e23467 100644
--- a/spec/stroma/dsl/generator_spec.rb
+++ b/spec/stroma/dsl/generator_spec.rb
@@ -56,9 +56,9 @@
       expect(base_class).to respond_to(:inherited)
     end
 
-    it "includes all registered DSL modules", :aggregate_failures do
-      expect(base_class.ancestors).to include(inputs_dsl)
-      expect(base_class.ancestors).to include(outputs_dsl)
+    it "does not include entry modules in base ancestors", :aggregate_failures do
+      expect(base_class.ancestors).not_to include(inputs_dsl)
+      expect(base_class.ancestors).not_to include(outputs_dsl)
     end
 
     it "creates stroma state" do
@@ -93,11 +93,21 @@ def self.included(base)
 
     let(:child_class) { Class.new(base_class) }
 
+    it "includes entry modules in child via interleaving", :aggregate_failures do
+      expect(child_class.ancestors).to include(inputs_dsl)
+      expect(child_class.ancestors).to include(outputs_dsl)
+    end
+
     it "applies hooks to child class" do
       expect(child_class.ancestors).to include(extension_module)
     end
 
-    it "child has extension method", :aggregate_failures do
+    it "positions hook adjacent to its target entry in child" do
+      ancestors = child_class.ancestors
+      expect(ancestors.index(extension_module)).to be < ancestors.index(inputs_dsl)
+    end
+
+    it "propagates extension callback to child", :aggregate_failures do
       expect(child_class).to respond_to(:extension_method)
       expect(child_class.extension_method).to eq(:extension_result)
     end
@@ -112,10 +122,127 @@ def self.included(base)
     end
   end
 
+  describe "multi-level inheritance" do
+    let(:base_class) do
+      mtx = matrix
+      Class.new { include mtx.dsl }
+    end
+
+    context "with hooks at one level" do
+      let(:auth_module) do
+        Module.new do
+          def self.included(base)
+            base.define_singleton_method(:auth_configured) { true }
+          end
+        end
+      end
+
+      let(:mid_class) do
+        base = base_class
+        auth = auth_module
+        Class.new(base) do
+          extensions do
+            before :inputs, auth
+          end
+        end
+      end
+
+      let(:leaf_class) { Class.new(mid_class) }
+
+      it "does not include entries in base", :aggregate_failures do
+        expect(base_class.ancestors).not_to include(inputs_dsl)
+        expect(base_class.ancestors).not_to include(outputs_dsl)
+      end
+
+      it "does not include entries in mid class", :aggregate_failures do
+        expect(mid_class.ancestors).not_to include(inputs_dsl)
+        expect(mid_class.ancestors).not_to include(outputs_dsl)
+      end
+
+      it "interleaves entries with hooks in leaf class", :aggregate_failures do
+        ancestors = leaf_class.ancestors
+
+        expect(ancestors).to include(inputs_dsl, outputs_dsl, auth_module)
+        expect(ancestors.index(auth_module)).to be < ancestors.index(inputs_dsl)
+      end
+
+      it "propagates hook callbacks to leaf" do
+        expect(leaf_class).to respond_to(:auth_configured)
+      end
+    end
+
+    context "with hooks at every level" do
+      let(:auth_module) { Module.new }
+      let(:logging_module) { Module.new }
+
+      let(:mid_class) do
+        base = base_class
+        auth = auth_module
+        Class.new(base) do
+          extensions do
+            before :inputs, auth
+          end
+        end
+      end
+
+      let(:leaf_class) do
+        mid = mid_class
+        logging = logging_module
+        Class.new(mid) do
+          extensions do
+            after :inputs, logging
+          end
+        end
+      end
+
+      it "includes hooks and entries from all levels", :aggregate_failures do
+        ancestors = Class.new(leaf_class).ancestors
+        expect(ancestors).to include(auth_module, logging_module, inputs_dsl, outputs_dsl)
+      end
+
+      it "positions before hook above entry in MRO" do
+        ancestors = Class.new(leaf_class).ancestors
+        expect(ancestors.index(auth_module)).to be < ancestors.index(inputs_dsl)
+      end
+
+      # Ruby's Module#include cannot position a new module below an inherited module.
+      # After hooks registered at parent level are placed above inherited entries in
+      # grandchild MRO. This does not affect phase execution order (controlled by
+      # the orchestrator), only the super call chain.
+      it "positions cross-level after hook above entry in MRO" do
+        ancestors = Class.new(leaf_class).ancestors
+        expect(ancestors.index(logging_module)).to be < ancestors.index(inputs_dsl)
+      end
+    end
+
+    context "when grandchild has no own hooks" do
+      let(:auth_module) { Module.new }
+
+      let(:mid_class) do
+        base = base_class
+        auth = auth_module
+        Class.new(base) do
+          extensions do
+            before :inputs, auth
+          end
+        end
+      end
+
+      let(:child_class) { Class.new(mid_class) }
+      let(:grandchild) { Class.new(child_class) }
+
+      it "propagates entries and hooks to grandchild", :aggregate_failures do
+        expect(grandchild.ancestors).to include(inputs_dsl)
+        expect(grandchild.ancestors).to include(outputs_dsl)
+        expect(grandchild.ancestors).to include(auth_module)
+      end
+    end
+  end
+
   describe "inheritance isolation" do
     let(:extension_module) { Module.new }
 
-    let(:parent_class) do
+    let(:base_class) do
       mtx = matrix
       ext = extension_module
       Class.new do
@@ -127,9 +254,9 @@ def self.included(base)
       end
     end
 
-    let(:child_class) { Class.new(parent_class) }
+    let(:child_class) { Class.new(base_class) }
 
-    it "child modifications do not affect parent", :aggregate_failures do
+    it "child modifications do not affect base", :aggregate_failures do
       child_extension = Module.new
 
       child_class.class_eval do
@@ -138,20 +265,20 @@ def self.included(base)
         end
       end
 
-      expect(parent_class.stroma.hooks.after(:outputs)).to be_empty
+      expect(base_class.stroma.hooks.after(:outputs)).to be_empty
       expect(child_class.stroma.hooks.after(:outputs)).not_to be_empty
     end
 
-    it "child inherits parent hooks", :aggregate_failures do
+    it "child inherits base hooks", :aggregate_failures do
       expect(child_class.stroma.hooks.before(:inputs).size).to eq(1)
       expect(child_class.ancestors).to include(extension_module)
     end
 
-    it "parent modifications after child creation do not affect child" do
+    it "base modifications after child creation do not affect child" do
       child_before_count = child_class.stroma.hooks.before(:outputs).size
       new_extension = Module.new
 
-      parent_class.class_eval do
+      base_class.class_eval do
         extensions do
           before :outputs, new_extension
         end
diff --git a/spec/stroma/hooks/applier_spec.rb b/spec/stroma/hooks/applier_spec.rb
index 93b98d6..2911ace 100644
--- a/spec/stroma/hooks/applier_spec.rb
+++ b/spec/stroma/hooks/applier_spec.rb
@@ -21,62 +21,181 @@
 
     before do
       hooks.add(:before, :inputs, before_extension)
+      described_class.apply!(target_class, hooks, matrix)
     end
 
     it "applies hooks via class method" do
-      described_class.apply!(target_class, hooks, matrix)
       expect(target_class.ancestors).to include(before_extension)
     end
   end
 
   describe "#apply!" do
-    it "does nothing when hooks empty" do
-      applier.apply!
-      expect(target_class.ancestors).not_to include(inputs_dsl)
+    context "when hooks are empty" do
+      it "does not modify target class ancestors" do
+        ancestors_before = target_class.ancestors.dup
+        applier.apply!
+        expect(target_class.ancestors).to eq(ancestors_before)
+      end
+
+      it "does not include entry extensions", :aggregate_failures do
+        applier.apply!
+        expect(target_class.ancestors).not_to include(inputs_dsl)
+        expect(target_class.ancestors).not_to include(outputs_dsl)
+      end
     end
 
-    context "with before hooks" do
-      let(:before_extension) { Module.new }
+    context "when entries are not in ancestors" do
+      context "with a before hook" do
+        let(:before_extension) { Module.new }
 
-      before do
-        hooks.add(:before, :inputs, before_extension)
+        before do
+          hooks.add(:before, :inputs, before_extension)
+          applier.apply!
+        end
+
+        it "positions before hook above entry in MRO" do
+          ancestors = target_class.ancestors
+          expect(ancestors.index(before_extension)).to be < ancestors.index(inputs_dsl)
+        end
+
+        it "includes all entries" do
+          expect(target_class.ancestors).to include(inputs_dsl, outputs_dsl)
+        end
       end
 
-      it "includes before hook extension" do
-        applier.apply!
-        expect(target_class.ancestors).to include(before_extension)
+      context "with an after hook" do
+        let(:after_extension) { Module.new }
+
+        before do
+          hooks.add(:after, :inputs, after_extension)
+          applier.apply!
+        end
+
+        it "positions after hook below entry in MRO" do
+          ancestors = target_class.ancestors
+          expect(ancestors.index(after_extension)).to be > ancestors.index(inputs_dsl)
+        end
       end
-    end
 
-    context "with after hooks" do
-      let(:after_extension) { Module.new }
+      context "with both before and after hooks" do
+        let(:before_extension) { Module.new }
+        let(:after_extension) { Module.new }
 
-      before do
-        hooks.add(:after, :outputs, after_extension)
+        before do
+          hooks.add(:before, :inputs, before_extension)
+          hooks.add(:after, :inputs, after_extension)
+          applier.apply!
+        end
+
+        it "positions before above and after below entry", :aggregate_failures do
+          ancestors = target_class.ancestors
+          expect(ancestors.index(before_extension)).to be < ancestors.index(inputs_dsl)
+          expect(ancestors.index(after_extension)).to be > ancestors.index(inputs_dsl)
+        end
       end
 
-      it "includes after hook extension" do
-        applier.apply!
-        expect(target_class.ancestors).to include(after_extension)
+      context "with multiple before hooks" do
+        let(:first_before) { Module.new }
+        let(:second_before) { Module.new }
+
+        before do
+          hooks.add(:before, :inputs, first_before)
+          hooks.add(:before, :inputs, second_before)
+          applier.apply!
+        end
+
+        it "first registered is outermost in MRO", :aggregate_failures do
+          ancestors = target_class.ancestors
+          expect(ancestors.index(first_before)).to be < ancestors.index(second_before)
+          expect(ancestors.index(second_before)).to be < ancestors.index(inputs_dsl)
+        end
       end
-    end
 
-    context "with multiple hooks" do # rubocop:disable RSpec/MultipleMemoizedHelpers
-      let(:before_inputs) { Module.new }
-      let(:after_inputs) { Module.new }
-      let(:before_outputs) { Module.new }
+      context "with multiple after hooks" do
+        let(:first_after) { Module.new }
+        let(:second_after) { Module.new }
 
+        before do
+          hooks.add(:after, :inputs, first_after)
+          hooks.add(:after, :inputs, second_after)
+          applier.apply!
+        end
+
+        it "first registered is closest to entry", :aggregate_failures do
+          ancestors = target_class.ancestors
+          expect(ancestors.index(inputs_dsl)).to be < ancestors.index(first_after)
+          expect(ancestors.index(first_after)).to be < ancestors.index(second_after)
+        end
+      end
+
+      context "with hooks for different entries" do
+        let(:before_inputs_extension) { Module.new }
+        let(:after_outputs_extension) { Module.new }
+
+        before do
+          hooks.add(:before, :inputs, before_inputs_extension)
+          hooks.add(:after, :outputs, after_outputs_extension)
+          applier.apply!
+        end
+
+        it "each hook is adjacent to its target entry", :aggregate_failures do
+          ancestors = target_class.ancestors
+          expect(ancestors.index(before_inputs_extension)).to be < ancestors.index(inputs_dsl)
+          expect(ancestors.index(after_outputs_extension)).to be > ancestors.index(outputs_dsl)
+        end
+      end
+    end
+
+    context "when entries are already in ancestors" do
       before do
-        hooks.add(:before, :inputs, before_inputs)
-        hooks.add(:after, :inputs, after_inputs)
-        hooks.add(:before, :outputs, before_outputs)
+        target_class.include(outputs_dsl)
+        target_class.include(inputs_dsl)
       end
 
-      it "applies all hooks", :aggregate_failures do
-        applier.apply!
-        expect(target_class.ancestors).to include(before_inputs)
-        expect(target_class.ancestors).to include(after_inputs)
-        expect(target_class.ancestors).to include(before_outputs)
+      context "with a before hook" do
+        let(:before_extension) { Module.new }
+
+        before do
+          hooks.add(:before, :inputs, before_extension)
+          applier.apply!
+        end
+
+        it "includes hook extensions" do
+          expect(target_class.ancestors).to include(before_extension)
+        end
+
+        it "does not duplicate entries in ancestors" do
+          expect(target_class.ancestors.count { |a| a == inputs_dsl }).to eq(1)
+        end
+      end
+
+      context "with an after hook" do
+        let(:after_extension) { Module.new }
+
+        before do
+          hooks.add(:after, :inputs, after_extension)
+          applier.apply!
+        end
+
+        it "includes after hook extensions" do
+          expect(target_class.ancestors).to include(after_extension)
+        end
+      end
+
+      context "with both before and after hooks" do
+        let(:before_extension) { Module.new }
+        let(:after_extension) { Module.new }
+
+        before do
+          hooks.add(:before, :inputs, before_extension)
+          hooks.add(:after, :inputs, after_extension)
+          applier.apply!
+        end
+
+        it "includes both hook types", :aggregate_failures do
+          expect(target_class.ancestors).to include(before_extension)
+          expect(target_class.ancestors).to include(after_extension)
+        end
       end
     end
   end