diff --git a/cmd/server.go b/cmd/server.go
index 3fc9ff1aaf..67a37fa8ac 100644
--- a/cmd/server.go
+++ b/cmd/server.go
@@ -32,8 +32,9 @@ import (
 // 3. Add your flag's description etc. to the stringFlags, intFlags, or boolFlags slices.
 const (
 	// Flag names.
-	AtlantisURLFlag     = "atlantis-url"
 	AllowForkPRsFlag    = "allow-fork-prs"
+	AllowRepoConfigFlag = "allow-repo-config"
+	AtlantisURLFlag     = "atlantis-url"
 	ConfigFlag          = "config"
 	DataDirFlag         = "data-dir"
 	GHHostnameFlag      = "gh-hostname"
@@ -142,6 +143,13 @@ var boolFlags = []boolFlag{
 		description:  "Allow Atlantis to run on pull requests from forks. A security issue for public repos.",
 		defaultValue: false,
 	},
+	{
+		name: AllowRepoConfigFlag,
+		description: "Allow repositories to use atlantis.yaml files to customize the commands Atlantis runs." +
+			" Should only be enabled in a trusted environment since it enables a pull request to run arbitrary commands" +
+			" on the Atlantis server.",
+		defaultValue: false,
+	},
 	{
 		name:         RequireApprovalFlag,
 		description:  "Require pull requests to be \"Approved\" before allowing the apply command to be run.",
@@ -298,8 +306,9 @@ func (s *ServerCmd) run() error {
 
 	// Config looks good. Start the server.
 	server, err := s.ServerCreator.NewServer(userConfig, server.Config{
-		AllowForkPRsFlag: AllowForkPRsFlag,
-		AtlantisVersion:  s.AtlantisVersion,
+		AllowForkPRsFlag:    AllowForkPRsFlag,
+		AllowRepoConfigFlag: AllowRepoConfigFlag,
+		AtlantisVersion:     s.AtlantisVersion,
 	})
 	if err != nil {
 		return errors.Wrap(err, "initializing server")
diff --git a/runatlantis.io/docs/atlantis-yaml-reference.md b/runatlantis.io/docs/atlantis-yaml-reference.md
index 9301f72aa5..a2fbe21755 100644
--- a/runatlantis.io/docs/atlantis-yaml-reference.md
+++ b/runatlantis.io/docs/atlantis-yaml-reference.md
@@ -9,6 +9,10 @@
 See [www.runatlantis.io/guide/atlantis-yaml-use-cases.html](../guide/atlantis-yaml-use-cases.html)
 :::
 
+## Enabling atlantis.yaml
+The atlantis server must be running with `--allow-repo-config` to allow Atlantis
+to use `atlantis.yaml` files.
+
 ## Example Using All Keys
 ```yaml
 version: 2
diff --git a/scripts/e2e.sh b/scripts/e2e.sh
index a1d3a44eea..02c6021658 100755
--- a/scripts/e2e.sh
+++ b/scripts/e2e.sh
@@ -8,7 +8,7 @@ ${CIRCLE_WORKING_DIRECTORY}/scripts/e2e-deps.sh
 cd "${CIRCLE_WORKING_DIRECTORY}/e2e"
 
 # start atlantis server in the background and wait for it to start
-./atlantis server --gh-user="$GITHUB_USERNAME" --gh-token="$GITHUB_PASSWORD" --data-dir="/tmp" --log-level="debug" --repo-whitelist="github.com/runatlantis/atlantis-tests" &> /tmp/atlantis-server.log &
+./atlantis server --gh-user="$GITHUB_USERNAME" --gh-token="$GITHUB_PASSWORD" --data-dir="/tmp" --log-level="debug" --repo-whitelist="github.com/runatlantis/atlantis-tests" --allow-repo-config &> /tmp/atlantis-server.log &
 sleep 2
 
 # start ngrok in the background and wait for it to start
diff --git a/server/events/command_runner_test.go b/server/events/command_runner_test.go
index 5f0d2ce4c0..0b1518c09c 100644
--- a/server/events/command_runner_test.go
+++ b/server/events/command_runner_test.go
@@ -41,7 +41,6 @@ var githubGetter *mocks.MockGithubPullGetter
 var gitlabGetter *mocks.MockGitlabMergeRequestGetter
 var ch events.DefaultCommandRunner
 var logBytes *bytes.Buffer
-var projectCommandRunner *mocks.MockProjectCommandRunner
 
 func setup(t *testing.T) {
 	RegisterMockTestingT(t)
diff --git a/server/events/project_command_builder.go b/server/events/project_command_builder.go
index a530ee31d9..549bbb3172 100644
--- a/server/events/project_command_builder.go
+++ b/server/events/project_command_builder.go
@@ -24,12 +24,14 @@ type ProjectCommandBuilder interface {
 }
 
 type DefaultProjectCommandBuilder struct {
-	ParserValidator  *yaml.ParserValidator
-	ProjectFinder    ProjectFinder
-	VCSClient        vcs.ClientProxy
-	WorkingDir       WorkingDir
-	WorkingDirLocker WorkingDirLocker
-	RequireApproval  bool
+	ParserValidator     *yaml.ParserValidator
+	ProjectFinder       ProjectFinder
+	VCSClient           vcs.ClientProxy
+	WorkingDir          WorkingDir
+	WorkingDirLocker    WorkingDirLocker
+	RequireApproval     bool
+	AllowRepoConfig     bool
+	AllowRepoConfigFlag string
 }
 
 type TerraformExec interface {
@@ -63,6 +65,9 @@ func (p *DefaultProjectCommandBuilder) BuildAutoplanCommands(ctx *CommandContext
 		ctx.Log.Info("found no %s file", yaml.AtlantisYAMLFilename)
 	} else {
 		ctx.Log.Info("successfully parsed %s file", yaml.AtlantisYAMLFilename)
+		if !p.AllowRepoConfig {
+			return nil, fmt.Errorf("%s files not allowed because Atlantis is not running with --%s", yaml.AtlantisYAMLFilename, p.AllowRepoConfigFlag)
+		}
 	}
 
 	// We'll need the list of modified files.
@@ -201,6 +206,9 @@ func (p *DefaultProjectCommandBuilder) getCfg(projectName string, dir string, wo
 	if !hasAtlantisYAML {
 		return nil, nil, nil
 	}
+	if !p.AllowRepoConfig {
+		return nil, nil, fmt.Errorf("%s files not allowed because Atlantis is not running with --%s", yaml.AtlantisYAMLFilename, p.AllowRepoConfigFlag)
+	}
 
 	// If they've specified a project by name we look it up. Otherwise we
 	// use the dir and workspace.
diff --git a/server/events/project_command_builder_test.go b/server/events/project_command_builder_test.go
index 111e790f40..1a50de40be 100644
--- a/server/events/project_command_builder_test.go
+++ b/server/events/project_command_builder_test.go
@@ -195,6 +195,7 @@ projects:
 				ParserValidator:  &yaml.ParserValidator{},
 				VCSClient:        vcsClient,
 				ProjectFinder:    &events.DefaultProjectFinder{},
+				AllowRepoConfig:  true,
 			}
 
 			ctxs, err := builder.BuildAutoplanCommands(&events.CommandContext{
@@ -416,6 +417,7 @@ projects:
 					ParserValidator:  &yaml.ParserValidator{},
 					VCSClient:        vcsClient,
 					ProjectFinder:    &events.DefaultProjectFinder{},
+					AllowRepoConfig:  true,
 				}
 
 				cmdCtx := &events.CommandContext{
diff --git a/server/events/terraform/terraform_client.go b/server/events/terraform/terraform_client.go
index ce290b13e2..bd2e6de704 100644
--- a/server/events/terraform/terraform_client.go
+++ b/server/events/terraform/terraform_client.go
@@ -42,7 +42,6 @@ type DefaultClient struct {
 const terraformPluginCacheDirName = "plugin-cache"
 
 // zeroPointNine constrains the version to be 0.9.*
-var zeroPointNine = MustConstraint(">=0.9,<0.10")
 var versionRegex = regexp.MustCompile("Terraform v(.*)\n")
 
 func NewClient(dataDir string) (*DefaultClient, error) {
diff --git a/server/events_controller_e2e_test.go b/server/events_controller_e2e_test.go
index 00048b63b4..b50215b3e8 100644
--- a/server/events_controller_e2e_test.go
+++ b/server/events_controller_e2e_test.go
@@ -270,11 +270,14 @@ func setupE2E(t *testing.T) (server.EventsController, *vcsmocks.MockClientProxy,
 		AllowForkPRs:             allowForkPRs,
 		AllowForkPRsFlag:         "allow-fork-prs",
 		ProjectCommandBuilder: &events.DefaultProjectCommandBuilder{
-			ParserValidator:  &yaml.ParserValidator{},
-			ProjectFinder:    &events.DefaultProjectFinder{},
-			VCSClient:        e2eVCSClient,
-			WorkingDir:       workingDir,
-			WorkingDirLocker: locker,
+			ParserValidator:     &yaml.ParserValidator{},
+			ProjectFinder:       &events.DefaultProjectFinder{},
+			VCSClient:           e2eVCSClient,
+			WorkingDir:          workingDir,
+			WorkingDirLocker:    locker,
+			AllowRepoConfigFlag: "allow-repo-config",
+			AllowRepoConfig:     true,
+			RequireApproval:     false,
 		},
 	}
 
diff --git a/server/server.go b/server/server.go
index efeddef900..0d7c595932 100644
--- a/server/server.go
+++ b/server/server.go
@@ -80,6 +80,7 @@ type Server struct {
 // the config is parsed from a YAML file.
 type UserConfig struct {
 	AllowForkPRs        bool   `mapstructure:"allow-fork-prs"`
+	AllowRepoConfig     bool   `mapstructure:"allow-repo-config"`
 	AtlantisURL         string `mapstructure:"atlantis-url"`
 	DataDir             string `mapstructure:"data-dir"`
 	GithubHostname      string `mapstructure:"gh-hostname"`
@@ -104,8 +105,9 @@ type UserConfig struct {
 
 // Config holds config for server that isn't passed in by the user.
 type Config struct {
-	AllowForkPRsFlag string
-	AtlantisVersion  string
+	AllowForkPRsFlag    string
+	AllowRepoConfigFlag string
+	AtlantisVersion     string
 }
 
 // WebhookConfig is nested within UserConfig. It's used to configure webhooks.
@@ -232,12 +234,14 @@ func NewServer(userConfig UserConfig, config Config) (*Server, error) {
 		AllowForkPRs:             userConfig.AllowForkPRs,
 		AllowForkPRsFlag:         config.AllowForkPRsFlag,
 		ProjectCommandBuilder: &events.DefaultProjectCommandBuilder{
-			ParserValidator:  &yaml.ParserValidator{},
-			ProjectFinder:    &events.DefaultProjectFinder{},
-			VCSClient:        vcsClient,
-			WorkingDir:       workingDir,
-			WorkingDirLocker: workingDirLocker,
-			RequireApproval:  userConfig.RequireApproval,
+			ParserValidator:     &yaml.ParserValidator{},
+			ProjectFinder:       &events.DefaultProjectFinder{},
+			VCSClient:           vcsClient,
+			WorkingDir:          workingDir,
+			WorkingDirLocker:    workingDirLocker,
+			RequireApproval:     userConfig.RequireApproval,
+			AllowRepoConfig:     userConfig.AllowRepoConfig,
+			AllowRepoConfigFlag: config.AllowRepoConfigFlag,
 		},
 		ProjectCommandRunner: &events.DefaultProjectCommandRunner{
 			Locker:           projectLocker,