diff --git a/CHANGELOG.md b/CHANGELOG.md
index ba13d35636..01e6cfdbf8 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -8,6 +8,10 @@ To install release candidates run `[sudo] gem install cocoapods --pre`
 
 ##### Enhancements
 
+* Integrate execution position for shell script phases  
+  [Dimitris Koutsogiorgas](https://github.com/dnkoutso)
+  [#7101](https://github.com/CocoaPods/CocoaPods/pull/7101)
+
 * Add support to integrate script phases from podspecs  
   [Dimitris Koutsogiorgas](https://github.com/dnkoutso)
   [#7092](https://github.com/CocoaPods/CocoaPods/pull/7092)
diff --git a/Gemfile.lock b/Gemfile.lock
index aa76f1d7e7..afb7d6155e 100644
--- a/Gemfile.lock
+++ b/Gemfile.lock
@@ -7,7 +7,7 @@ GIT
 
 GIT
   remote: https://github.com/CocoaPods/Core.git
-  revision: 3f98bce41fd8eb6d385441eef4e5611665d13e64
+  revision: 153c5dfdd02eaac8bec160f6a3b3bc49b07ecf48
   branch: master
   specs:
     cocoapods-core (1.4.0.beta.1)
diff --git a/lib/cocoapods/installer/user_project_integrator/target_integrator.rb b/lib/cocoapods/installer/user_project_integrator/target_integrator.rb
index 144781a1d0..acc2e43ab1 100644
--- a/lib/cocoapods/installer/user_project_integrator/target_integrator.rb
+++ b/lib/cocoapods/installer/user_project_integrator/target_integrator.rb
@@ -165,21 +165,29 @@ def create_or_update_user_script_phases(script_phases, native_target)
             end
             # Create or update the ones that are expected to be.
             script_phases.each do |td_script_phase|
-              phase = TargetIntegrator.create_or_update_build_phase(native_target, USER_BUILD_PHASE_PREFIX + td_script_phase[:name])
+              name_with_prefix = USER_BUILD_PHASE_PREFIX + td_script_phase[:name]
+              phase = TargetIntegrator.create_or_update_build_phase(native_target, name_with_prefix)
               phase.shell_script = td_script_phase[:script]
               phase.shell_path = td_script_phase[:shell_path] if td_script_phase.key?(:shell_path)
               phase.input_paths = td_script_phase[:input_files] if td_script_phase.key?(:input_files)
               phase.output_paths = td_script_phase[:output_files] if td_script_phase.key?(:output_files)
               phase.show_env_vars_in_log = td_script_phase[:show_env_vars_in_log] ? '1' : '0' if td_script_phase.key?(:show_env_vars_in_log)
-            end
-            # Move script phases to their correct index if the order has changed.
-            offset = native_target.build_phases.count - script_phases.count
-            script_phases.each_with_index do |td_script_phase, index|
-              current_index = native_target.build_phases.index do |bp|
-                bp.is_a?(Xcodeproj::Project::Object::PBXShellScriptBuildPhase) && bp.name.sub(USER_BUILD_PHASE_PREFIX, '') == td_script_phase[:name]
+
+              execution_position = td_script_phase[:execution_position]
+              unless execution_position == :any
+                compile_build_phase_index = native_target.build_phases.index do |bp|
+                  bp.is_a?(Xcodeproj::Project::Object::PBXSourcesBuildPhase)
+                end
+                unless compile_build_phase_index.nil?
+                  script_phase_index = native_target.build_phases.index do |bp|
+                    bp.is_a?(Xcodeproj::Project::Object::PBXShellScriptBuildPhase) && !bp.name.nil? && bp.name == name_with_prefix
+                  end
+                  if (execution_position == :before_compile && script_phase_index > compile_build_phase_index) ||
+                    (execution_position == :after_compile && script_phase_index < compile_build_phase_index)
+                    native_target.build_phases.move_from(script_phase_index, compile_build_phase_index)
+                  end
+                end
               end
-              expected_index = offset + index
-              native_target.build_phases.insert(expected_index, native_target.build_phases.delete_at(current_index)) if current_index != expected_index
             end
           end
         end
diff --git a/spec/unit/installer/user_project_integrator/target_integrator_spec.rb b/spec/unit/installer/user_project_integrator/target_integrator_spec.rb
index 20174004dc..25f4d69fc6 100644
--- a/spec/unit/installer/user_project_integrator/target_integrator_spec.rb
+++ b/spec/unit/installer/user_project_integrator/target_integrator_spec.rb
@@ -388,32 +388,50 @@ module Pod
           target.shell_script_build_phases.find { |bp| bp.name == @user_script_phase_name }.should.be.nil
         end
 
-        it 'moves custom shell scripts to their correct index' do
-          shell_script_one = { :name => 'Custom Script', :script => 'echo "Hello World"' }
+        it 'moves custom shell scripts according to their execution position' do
+          shell_script_one = { :name => 'Custom Script', :script => 'echo "Hello World"', :execution_position => :before_compile }
           shell_script_two = { :name => 'Custom Script 2', :script => 'echo "Hello Aliens"' }
           @pod_bundle.target_definition.stubs(:script_phases).returns([shell_script_one, shell_script_two])
           @target_integrator.integrate!
           target = @target_integrator.send(:native_targets).first
-          target.shell_script_build_phases.map(&:name).should == [
+          target.build_phases.map(&:display_name).should == [
             '[CP] Check Pods Manifest.lock',
+            '[CP-User] Custom Script',
+            'Sources',
+            'Frameworks',
+            'Resources',
             '[CP] Embed Pods Frameworks',
             '[CP] Copy Pods Resources',
-            '[CP-User] Custom Script',
             '[CP-User] Custom Script 2',
           ]
-          shell_script_one_uuid = target.shell_script_build_phases[3].uuid
-          shell_script_two_uuid = target.shell_script_build_phases[4].uuid
-          @pod_bundle.target_definition.stubs(:script_phases).returns([shell_script_two, shell_script_one])
+          shell_script_one = { :name => 'Custom Script', :script => 'echo "Hello World"', :execution_position => :after_compile }
+          shell_script_two = { :name => 'Custom Script 2', :script => 'echo "Hello Aliens"', :execution_position => :before_compile }
+          @pod_bundle.target_definition.stubs(:script_phases).returns([shell_script_one, shell_script_two])
           @target_integrator.integrate!
-          target.shell_script_build_phases.map(&:name).should == [
+          target.build_phases.map(&:display_name).should == [
             '[CP] Check Pods Manifest.lock',
+            '[CP-User] Custom Script 2',
+            'Sources',
+            '[CP-User] Custom Script',
+            'Frameworks',
+            'Resources',
             '[CP] Embed Pods Frameworks',
             '[CP] Copy Pods Resources',
+          ]
+          shell_script_one = { :name => 'Custom Script', :script => 'echo "Hello World"' }
+          shell_script_two = { :name => 'Custom Script 2', :script => 'echo "Hello Aliens"' }
+          @pod_bundle.target_definition.stubs(:script_phases).returns([shell_script_one, shell_script_two])
+          @target_integrator.integrate!
+          target.build_phases.map(&:display_name).should == [
+            '[CP] Check Pods Manifest.lock',
             '[CP-User] Custom Script 2',
+            'Sources',
             '[CP-User] Custom Script',
+            'Frameworks',
+            'Resources',
+            '[CP] Embed Pods Frameworks',
+            '[CP] Copy Pods Resources',
           ]
-          target.shell_script_build_phases[3].uuid.should == shell_script_two_uuid
-          target.shell_script_build_phases[4].uuid.should == shell_script_one_uuid
         end
 
         it 'adds, removes and moves custom shell script phases' do
@@ -424,8 +442,11 @@ module Pod
           @pod_bundle.target_definition.stubs(:script_phases).returns([shell_script_one, shell_script_two, shell_script_three])
           @target_integrator.integrate!
           target = @target_integrator.send(:native_targets).first
-          target.shell_script_build_phases.map(&:name).should == [
+          target.build_phases.map(&:display_name).should == [
             '[CP] Check Pods Manifest.lock',
+            'Sources',
+            'Frameworks',
+            'Resources',
             '[CP] Embed Pods Frameworks',
             '[CP] Copy Pods Resources',
             '[CP-User] Custom Script',
@@ -434,8 +455,11 @@ module Pod
           ]
           @pod_bundle.target_definition.stubs(:script_phases).returns([shell_script_two, shell_script_four])
           @target_integrator.integrate!
-          target.shell_script_build_phases.map(&:name).should == [
+          target.build_phases.map(&:display_name).should == [
             '[CP] Check Pods Manifest.lock',
+            'Sources',
+            'Frameworks',
+            'Resources',
             '[CP] Embed Pods Frameworks',
             '[CP] Copy Pods Resources',
             '[CP-User] Custom Script 2',
@@ -449,8 +473,11 @@ module Pod
           target.new_shell_script_build_phase('User Script Phase 1')
           target.new_shell_script_build_phase('User Script Phase 2')
           @target_integrator.integrate!
-          target.shell_script_build_phases.map(&:name).should == [
+          target.build_phases.map(&:display_name).should == [
             '[CP] Check Pods Manifest.lock',
+            'Sources',
+            'Frameworks',
+            'Resources',
             'User Script Phase 1',
             'User Script Phase 2',
             '[CP] Embed Pods Frameworks',
@@ -459,8 +486,11 @@ module Pod
           ]
           @pod_bundle.target_definition.stubs(:script_phases).returns([])
           @target_integrator.integrate!
-          target.shell_script_build_phases.map(&:name).should == [
+          target.build_phases.map(&:display_name).should == [
             '[CP] Check Pods Manifest.lock',
+            'Sources',
+            'Frameworks',
+            'Resources',
             'User Script Phase 1',
             'User Script Phase 2',
             '[CP] Embed Pods Frameworks',