diff --git a/middleman-core/lib/middleman-core/application.rb b/middleman-core/lib/middleman-core/application.rb
index 1ad45f2b..ab1b9798 100644
--- a/middleman-core/lib/middleman-core/application.rb
+++ b/middleman-core/lib/middleman-core/application.rb
@@ -18,6 +18,8 @@ require 'middleman-core/logger'
 require 'middleman-core/sitemap/store'
 
 require 'middleman-core/configuration'
+
+require 'middleman-core/extension_manager'
 require 'middleman-core/core_extensions'
 
 require 'middleman-core/config_context'
@@ -27,9 +29,6 @@ require 'middleman-core/template_renderer'
 # Rack Request
 require 'middleman-core/core_extensions/request'
 
-# Custom Extension API and config.rb handling
-require 'middleman-core/core_extensions/extensions'
-
 # Core Middleman Class
 module Middleman
   class Application
@@ -156,8 +155,13 @@ module Middleman
       }
     }, 'Callbacks that can exclude paths from the sitemap'
 
-    # Activate custom features and extensions
-    include Middleman::CoreExtensions::Extensions
+    define_hook :initialized
+    define_hook :instance_available
+    define_hook :after_configuration
+    define_hook :before_configuration
+
+    config.define_setting :autoload_sprockets, true, 'Automatically load sprockets at startup?'
+    config[:autoload_sprockets] = (ENV['AUTOLOAD_SPROCKETS'] == 'true') if ENV['AUTOLOAD_SPROCKETS']
 
     # Basic Rack Request Handling
     include Middleman::CoreExtensions::Request
@@ -166,9 +170,7 @@ module Middleman
     include Middleman::CoreExtensions::Rendering
 
     # Reference to Logger singleton
-    def logger
-      ::Middleman::Logger.singleton
-    end
+    def_delegator :"::Middleman::Logger", :singleton, :logger
 
     # New container for config.rb commands
     attr_reader :config_context
@@ -181,11 +183,19 @@ module Middleman
 
     attr_reader :template_context_class
 
+    # Hack to get a sandboxed copy of these helpers for overriding similar methods inside Markdown renderers.
     attr_reader :generic_template_context
     def_delegators :@generic_template_context, :link_to, :image_tag, :asset_path
 
+    attr_reader :extensions
+
     # Initialize the Middleman project
-    def initialize
+    def initialize(&block)
+      self.class.inst = self
+
+      # Search the root of the project for required files
+      $LOAD_PATH.unshift(root) unless $LOAD_PATH.include?(root)
+
       @template_context_class = Class.new(Middleman::TemplateContext)
       @generic_template_context = @template_context_class.new(self)
       @config_context = ConfigContext.new(self, @template_context_class)
@@ -196,7 +206,8 @@ module Middleman
       # Setup the default values from calls to set before initialization
       self.class.config.load_settings(self.class.superclass.config.all_settings)
 
-      ::Middleman::Extensions.auto_activate(:before_sitemap, self)
+      @extensions = ::Middleman::ExtensionManager.new(self)
+      @extensions.auto_activate(:before_sitemap)
 
       # Initialize the Sitemap
       @sitemap = ::Middleman::Sitemap::Store.new(self)
@@ -208,7 +219,60 @@ module Middleman
 
       config[:source] = ENV['MM_SOURCE'] if ENV['MM_SOURCE']
 
-      super
+      ::Middleman::Extension.clear_after_extension_callbacks
+
+      @extensions.auto_activate(:before_configuration)
+
+      if config[:autoload_sprockets]
+        begin
+          require 'middleman-sprockets'
+          activate :sprockets
+        rescue LoadError
+          # It's OK if somebody is using middleman-core without middleman-sprockets
+        end
+      end
+
+      run_hook :initialized
+
+      run_hook :before_configuration
+
+      evaluate_configuration(&block)
+
+      run_hook :instance_available
+
+      # This is for making the tests work - since the tests
+      # don't completely reload middleman, I18n.load_path can get
+      # polluted with paths from other test app directories that don't
+      # exist anymore.
+      if ENV['TEST']
+        ::I18n.load_path.delete_if { |path| path =~ %r{tmp/aruba} }
+        ::I18n.reload!
+      end
+
+      run_hook :after_configuration
+      config_context.execute_after_configuration_callbacks
+
+      @extensions.activate_all
+    end
+
+    def evaluate_configuration(&block)
+      # Evaluate a passed block if given
+      config_context.instance_exec(&block) if block_given?
+
+      # Check for and evaluate local configuration in `config.rb`
+      local_config = File.join(root, 'config.rb')
+      if File.exist? local_config
+        logger.debug '== Reading: Local config'
+        config_context.instance_eval File.read(local_config), local_config, 1
+      end
+
+      env_config = File.join(root, 'environments', "#{config[:environment]}.rb")
+      if File.exist? env_config
+        logger.debug "== Reading: #{config[:environment]} config"
+        config_context.instance_eval File.read(env_config), env_config, 1
+      end
+
+      config_context.execute_configure_callbacks(config[:environment])
     end
 
     def add_to_instance(name, &func)
diff --git a/middleman-core/lib/middleman-core/config_context.rb b/middleman-core/lib/middleman-core/config_context.rb
index 92368760..caeebd51 100644
--- a/middleman-core/lib/middleman-core/config_context.rb
+++ b/middleman-core/lib/middleman-core/config_context.rb
@@ -5,7 +5,8 @@ module Middleman
     attr_reader :app
 
     # Whitelist methods that can reach out.
-    def_delegators :@app, :config, :logger, :activate, :use, :map, :mime_type, :data, :files, :root
+    def_delegators :@app, :config, :logger, :use, :map, :mime_type, :data, :files, :root
+    def_delegator :"@app.extensions", :activate
 
     def initialize(app, template_context_class)
       @app = app
diff --git a/middleman-core/lib/middleman-core/core_extensions/extensions.rb b/middleman-core/lib/middleman-core/core_extensions/extensions.rb
deleted file mode 100644
index 9c62edf6..00000000
--- a/middleman-core/lib/middleman-core/core_extensions/extensions.rb
+++ /dev/null
@@ -1,162 +0,0 @@
-module Middleman
-  module CoreExtensions
-    # The Extensions core module provides basic configurability to Middleman projects:
-    #
-    # * It loads and evaluates `config.rb`.
-    # * It defines lifecycle hooks for extensions and `config.rb` to use.
-    # * It provides the {#activate} method for use in `config.rb`.
-    module Extensions
-      def self.included(app)
-        app.define_hook :initialized
-        app.define_hook :instance_available
-        app.define_hook :after_configuration
-        app.define_hook :before_configuration
-
-        app.config.define_setting :autoload_sprockets, true, 'Automatically load sprockets at startup?'
-        app.config[:autoload_sprockets] = (ENV['AUTOLOAD_SPROCKETS'] == 'true') if ENV['AUTOLOAD_SPROCKETS']
-
-        app.extend ClassMethods
-        app.def_delegator :"self.class", :configure
-      end
-
-      module ClassMethods
-        # Register a block to run only in a specific environment.
-        #
-        # @example
-        #    # Only minify when building
-        #    configure :production do
-        #      activate :minify_javascript
-        #    end
-        #
-        # @param [String, Symbol] env The environment to run in
-        # @return [void]
-        def configure(env, &block)
-          send("#{env}_config", &block)
-        end
-      end
-
-      # Activate an extension, optionally passing in options.
-      # This method is typically used from a project's `config.rb`.
-      #
-      # @example Activate an extension with no options
-      #     activate :lorem
-      #
-      # @example Activate an extension, with options
-      #     activate :minify_javascript, inline: true
-      #
-      # @example Use a block to configure extension options
-      #     activate :minify_javascript do |opts|
-      #       opts.ignore += ['*-test.js']
-      #     end
-      #
-      # @param [Symbol] ext_name The name of thed extension to activate
-      # @param [Hash] options Options to pass to the extension
-      # @yield [Middleman::Configuration::ConfigurationManager] Extension options that can be modified before the extension is initialized.
-      # @return [void]
-      def activate(ext_name, options={}, &block)
-        extension = ::Middleman::Extensions.load(ext_name)
-        logger.debug "== Activating: #{ext_name}"
-
-        if extension.supports_multiple_instances?
-          extensions[ext_name] ||= {}
-          key = "instance_#{extensions[ext_name].keys.length}"
-          extensions[ext_name][key] = extension.new(self.class, options, &block)
-        elsif extensions.key?(ext_name)
-          raise "#{ext_name} has already been activated and cannot be re-activated."
-        else
-          extensions[ext_name] = extension.new(self.class, options, &block)
-        end
-      end
-
-      # A hash of all activated extensions, indexed by their name. If an extension supports multiple
-      # instances, it will be stored as a hash of instances instead of just the instance.
-      #
-      # @return [Hash{Symbol => Middleman::Extension, Hash{String => Middleman::Extension}}]
-      def extensions
-        @extensions ||= {}
-      end
-
-      # Override application initialization to load `config.rb` and to call lifecycle hooks.
-      def initialize(&block)
-        self.class.inst = self
-
-        # Search the root of the project for required files
-        $LOAD_PATH.unshift(root) unless $LOAD_PATH.include?(root)
-
-        super
-
-        ::Middleman::Extension.clear_after_extension_callbacks
-
-        ::Middleman::Extensions.auto_activate(:before_configuration, self)
-
-        if config[:autoload_sprockets]
-          begin
-            require 'middleman-sprockets'
-            activate :sprockets
-          rescue LoadError
-            # It's OK if somebody is using middleman-core without middleman-sprockets
-          end
-        end
-
-        run_hook :initialized
-
-        run_hook :before_configuration
-
-        # Evaluate a passed block if given
-        config_context.instance_exec(&block) if block_given?
-
-        # Check for and evaluate local configuration in `config.rb`
-        local_config = File.join(root, 'config.rb')
-        if File.exist? local_config
-          logger.debug '== Reading: Local config'
-          config_context.instance_eval File.read(local_config), local_config, 1
-        end
-
-        env_config = File.join(root, 'environments', "#{config[:environment]}.rb")
-        if File.exist? env_config
-          logger.debug "== Reading: #{config[:environment]} config"
-          config_context.instance_eval File.read(env_config), env_config, 1
-        end
-
-        config_context.execute_configure_callbacks(config[:environment])
-
-        run_hook :instance_available
-
-        # This is for making the tests work - since the tests
-        # don't completely reload middleman, I18n.load_path can get
-        # polluted with paths from other test app directories that don't
-        # exist anymore.
-        if ENV['TEST']
-          ::I18n.load_path.delete_if { |path| path =~ %r{tmp/aruba} }
-          ::I18n.reload!
-        end
-
-        run_hook :after_configuration
-        config_context.execute_after_configuration_callbacks
-
-        extension_instances = []
-        logger.debug 'Loaded extensions:'
-        extensions.each do |ext_name, ext|
-          if ext.is_a?(Hash)
-            ext.each do |instance_key, instance|
-              logger.debug "== Extension: #{ext_name} #{instance_key}"
-              extension_instances << instance
-            end
-          else
-            logger.debug "== Extension: #{ext_name}"
-            extension_instances << ext
-          end
-        end
-
-        extension_instances.each do |ext|
-          # Forward Extension helpers to TemplateContext
-          Array(ext.class.defined_helpers).each do |m|
-            @template_context_class.send(:include, m)
-          end
-
-          ::Middleman::Extension.activated_extension(ext)
-        end
-      end
-    end
-  end
-end
diff --git a/middleman-core/lib/middleman-core/extension_manager.rb b/middleman-core/lib/middleman-core/extension_manager.rb
new file mode 100644
index 00000000..169646e5
--- /dev/null
+++ b/middleman-core/lib/middleman-core/extension_manager.rb
@@ -0,0 +1,73 @@
+module Middleman
+  class ExtensionManager
+    extend Forwardable
+    def_delegator :"::Middleman::Logger", :singleton, :logger
+    def_delegators :@activated, :[]
+
+    def initialize(app)
+      @app = app
+      @activated = {}
+    end
+
+    def auto_activate(key)
+      ::Middleman::Extensions.auto_activate(key, @app)
+    end
+
+    # Activate an extension, optionally passing in options.
+    # This method is typically used from a project's `config.rb`.
+    #
+    # @example Activate an extension with no options
+    #     activate :lorem
+    #
+    # @example Activate an extension, with options
+    #     activate :minify_javascript, inline: true
+    #
+    # @example Use a block to configure extension options
+    #     activate :minify_javascript do |opts|
+    #       opts.ignore += ['*-test.js']
+    #     end
+    #
+    # @param [Symbol] ext_name The name of thed extension to activate
+    # @param [Hash] options Options to pass to the extension
+    # @yield [Middleman::Configuration::ConfigurationManager] Extension options that can be modified before the extension is initialized.
+    # @return [void]
+    def activate(ext_name, options={}, &block)
+      extension = ::Middleman::Extensions.load(ext_name)
+      logger.debug "== Activating: #{ext_name}"
+
+      if extension.supports_multiple_instances?
+        @activated[ext_name] ||= {}
+        key = "instance_#{@activated[ext_name].keys.length}"
+        @activated[ext_name][key] = extension.new(@app.class, options, &block)
+      elsif @activated.key?(ext_name)
+        raise "#{ext_name} has already been activated and cannot be re-activated."
+      else
+        @activated[ext_name] = extension.new(@app.class, options, &block)
+      end
+    end
+
+    def activate_all
+      logger.debug 'Loaded extensions:'
+      instances = @activated.each_with_object([]) do |(ext_name, ext), sum|
+        if ext.is_a?(Hash)
+          ext.each do |instance_key, instance|
+            logger.debug "== Extension: #{ext_name} #{instance_key}"
+            sum << instance
+          end
+        else
+          logger.debug "== Extension: #{ext_name}"
+          sum << ext
+        end
+      end
+
+      instances.each do |ext|
+        # Forward Extension helpers to TemplateContext
+        Array(ext.class.defined_helpers).each do |m|
+          @app.template_context_class.send(:include, m)
+        end
+
+        ::Middleman::Extension.activated_extension(ext)
+      end
+    end
+  end
+end
diff --git a/middleman-core/lib/middleman-core/extensions.rb b/middleman-core/lib/middleman-core/extensions.rb
index dac9ea75..37690957 100644
--- a/middleman-core/lib/middleman-core/extensions.rb
+++ b/middleman-core/lib/middleman-core/extensions.rb
@@ -116,7 +116,7 @@ module Middleman
         @auto_activate[group].each do |descriptor|
           next unless descriptor[:modes] == :all || descriptor[:modes].include?(app.config[:mode])
 
-          app.activate descriptor[:name]
+          app.extensions.activate descriptor[:name]
         end
       end
     end