diff --git a/lib/bundler/cli.rb b/lib/bundler/cli.rb
index affd7a78c11..6aad0fc8222 100644
--- a/lib/bundler/cli.rb
+++ b/lib/bundler/cli.rb
@@ -61,11 +61,6 @@ def initialize(*args)
       end
     end
 
-    def self.deprecated_option(*args, &blk)
-      return if Bundler.feature_flag.forget_cli_options?
-      method_option(*args, &blk)
-    end
-
     check_unknown_options!(:except => [:config, :exec])
     stop_on_unknown_option! :exec
 
@@ -142,7 +137,7 @@ def self.handle_no_command_error(command, has_namespace = $thor_runner)
       Gemfile to a gem with a gemspec, the --gemspec option will automatically add each
       dependency listed in the gemspec file to the newly created Gemfile.
     D
-    deprecated_option "gemspec", :type => :string, :banner => "Use the specified .gemspec to create the Gemfile"
+    method_option "gemspec", :type => :string, :banner => "Use the specified .gemspec to create the Gemfile"
     def init
       require "bundler/cli/init"
       Init.new(options.dup).run
@@ -188,13 +183,13 @@ def remove(*gems)
 
       If the bundle has already been installed, bundler will tell you so and then exit.
     D
-    deprecated_option "binstubs", :type => :string, :lazy_default => "bin", :banner =>
+    method_option "binstubs", :type => :string, :lazy_default => "bin", :banner =>
       "Generate bin stubs for bundled gems to ./bin"
-    deprecated_option "clean", :type => :boolean, :banner =>
+    method_option "clean", :type => :boolean, :banner =>
       "Run bundle clean automatically after install"
-    deprecated_option "deployment", :type => :boolean, :banner =>
+    method_option "deployment", :type => :boolean, :banner =>
       "Install using defaults tuned for deployment environments"
-    deprecated_option "frozen", :type => :boolean, :banner =>
+    method_option "frozen", :type => :boolean, :banner =>
       "Do not allow the Gemfile.lock to be updated after this install"
     method_option "full-index", :type => :boolean, :banner =>
       "Fall back to using the single-file index of all gems"
@@ -204,32 +199,37 @@ def remove(*gems)
       "Specify the number of jobs to run in parallel"
     method_option "local", :type => :boolean, :banner =>
       "Do not attempt to fetch gems remotely and use the gem cache instead"
-    deprecated_option "no-cache", :type => :boolean, :banner =>
+    method_option "no-cache", :type => :boolean, :banner =>
       "Don't update the existing gem cache."
     method_option "redownload", :type => :boolean, :aliases => "--force", :banner =>
       "Force downloading every gem."
-    deprecated_option "no-prune", :type => :boolean, :banner =>
+    method_option "no-prune", :type => :boolean, :banner =>
       "Don't remove stale gems from the cache."
-    deprecated_option "path", :type => :string, :banner =>
+    method_option "path", :type => :string, :banner =>
       "Specify a different path than the system default ($BUNDLE_PATH or $GEM_HOME). Bundler will remember this value for future installs on this machine"
     method_option "quiet", :type => :boolean, :banner =>
       "Only output warnings and errors."
-    deprecated_option "shebang", :type => :string, :banner =>
+    method_option "shebang", :type => :string, :banner =>
       "Specify a different shebang executable name than the default (usually 'ruby')"
     method_option "standalone", :type => :array, :lazy_default => [], :banner =>
       "Make a bundle that can work without the Bundler runtime"
-    deprecated_option "system", :type => :boolean, :banner =>
+    method_option "system", :type => :boolean, :banner =>
       "Install to the system location ($BUNDLE_PATH or $GEM_HOME) even if the bundle was previously installed somewhere else for this application"
     method_option "trust-policy", :alias => "P", :type => :string, :banner =>
       "Gem trust policy (like gem install -P). Must be one of " +
         Bundler.rubygems.security_policy_keys.join("|")
-    deprecated_option "without", :type => :array, :banner =>
+    method_option "without", :type => :array, :banner =>
       "Exclude gems that are part of the specified named group."
-    deprecated_option "with", :type => :array, :banner =>
+    method_option "with", :type => :array, :banner =>
       "Include gems that are part of the specified named group."
     map "i" => "install"
     def install
       SharedHelpers.major_deprecation(2, "The `--force` option has been renamed to `--redownload`") if ARGV.include?("--force")
+
+      %w[clean deployment frozen no-cache no-prune path shebang system without with].each do |option|
+        remembered_flag_deprecation(option)
+      end
+
       require "bundler/cli/install"
       Bundler.settings.temporary(:no_install => false) do
         Install.new(options.dup).run
@@ -786,5 +786,22 @@ def warn_on_outdated_bundler
     rescue RuntimeError
       nil
     end
+
+    def remembered_flag_deprecation(name)
+      option = current_command.options[name]
+      flag_name = option.switch_name
+
+      name_index = ARGV.find {|arg| flag_name == arg }
+      return unless name_index
+
+      value = options[name]
+      value = value.join(" ").to_s if option.type == :array
+
+      Bundler::SharedHelpers.major_deprecation 2,\
+        "The `#{flag_name}` flag is deprecated because it relied on being " \
+        "remembered accross bundler invokations, which bundler will no longer " \
+        "do in future versions. Instead please use `bundle config #{name} " \
+        "'#{value}'`, and stop using this flag"
+    end
   end
 end
diff --git a/lib/bundler/feature_flag.rb b/lib/bundler/feature_flag.rb
index 8b7b836e424..e01676f97d2 100644
--- a/lib/bundler/feature_flag.rb
+++ b/lib/bundler/feature_flag.rb
@@ -38,7 +38,7 @@ def self.settings_method(name, key, &default)
     settings_flag(:deployment_means_frozen) { bundler_2_mode? }
     settings_flag(:disable_multisource) { bundler_2_mode? }
     settings_flag(:error_on_stderr) { bundler_2_mode? }
-    settings_flag(:forget_cli_options) { bundler_2_mode? }
+    settings_flag(:forget_cli_options) { bundler_3_mode? }
     settings_flag(:global_path_appends_ruby_scope) { bundler_2_mode? }
     settings_flag(:global_gem_cache) { bundler_2_mode? }
     settings_flag(:init_gems_rb) { bundler_2_mode? }
diff --git a/lib/bundler/settings.rb b/lib/bundler/settings.rb
index bed5c5604e9..c708659e1cc 100644
--- a/lib/bundler/settings.rb
+++ b/lib/bundler/settings.rb
@@ -116,11 +116,19 @@ def set_command_option(key, value)
           "bundle config set #{key} #{Array(value).join(":")}"
         end
 
-        Bundler::SharedHelpers.major_deprecation 2,\
-          "flags passed to commands " \
-          "will no longer be automatically remembered. Instead please set flags " \
-          "you want remembered between commands using `bundle config set " \
-          "<setting name> <setting value>`, i.e. `#{command}`"
+        unless Bundler.settings[:forget_cli_options] == false
+          Bundler::SharedHelpers.major_deprecation 3,\
+            "flags passed to commands " \
+            "will no longer be automatically remembered. Instead please set flags " \
+            "you want remembered between commands using `bundle config set " \
+            "<setting name> <setting value>`, i.e. `#{command}`. Once you are " \
+            "ready for the new behavior, use `bundle config set forget_cli_options " \
+            "true` to get rid of this message. Or if you want to get rid of " \
+            "this message and stick with the old behavior for now, run " \
+            "`bundle config set forget_cli_options false`, but keep in mind " \
+            "that this behavior will be fully removed in future versions of " \
+            "bundler."
+        end
 
         set_local(key, value)
       end
diff --git a/spec/other/major_deprecation_spec.rb b/spec/other/major_deprecation_spec.rb
index 5175e8d4c8d..de9c05ec672 100644
--- a/spec/other/major_deprecation_spec.rb
+++ b/spec/other/major_deprecation_spec.rb
@@ -111,7 +111,7 @@
     end
 
     context "with flags" do
-      xit "should print a deprecation warning about autoremembering flags" do
+      it "should print a deprecation warning about autoremembering flags", :bundler => "3" do
         install_gemfile <<-G, :path => "vendor/bundle"
           source "file://#{gem_repo1}"
           gem "rack"
@@ -121,6 +121,42 @@
           "flags passed to commands will no longer be automatically remembered."
         )
       end
+
+      {
+        :clean => true,
+        :deployment => true,
+        :frozen => true,
+        :"no-cache" => true,
+        :"no-prune" => true,
+        :path => "vendor/bundle",
+        :shebang => "ruby27",
+        :system => true,
+        :without => "development",
+        :with => "development",
+      }.each do |name, value|
+        flag_name = "--#{name}"
+
+        context "with the #{flag_name} flag", :bundler => "2" do
+          it "should print a deprecation warning" do
+            bundle "install #{flag_name} #{value}"
+
+            expect(warnings).to have_major_deprecation(
+              "The `#{flag_name}` flag is deprecated because it relied on " \
+              "being remembered accross bundler invokations, which bundler " \
+              "will no longer do in future versions. Instead please use " \
+              "`bundle config #{name} '#{value}'`, and stop using this flag"
+            )
+          end
+        end
+
+        context "with the #{flag_name} flag", :bundler => "< 2" do
+          it "should not print a deprecation warning" do
+            bundle "install #{flag_name} #{value}"
+
+            expect(warnings).not_to have_major_deprecation
+          end
+        end
+      end
     end
   end