diff --git a/README.md b/README.md
index 11807597dd..2ba4db7a11 100644
--- a/README.md
+++ b/README.md
@@ -21,7 +21,8 @@ Available commands are:
   meta-data  Get/set data from Buildkite jobs
   pipeline   Make changes to the pipeline of the currently running build
   step       Make changes to a step (this includes any jobs that were created from the step)
-  bootstrap  Run a Buildkite job locally
+  bootstrap  [DEPRECATED] Run a Buildkite job locally
+  exec-job   Run a Buildkite job locally
   help       Shows a list of commands or help for one command
 
 Use "buildkite-agent <command> --help" for more information about a command.
diff --git a/clicommand/agent_start.go b/clicommand/agent_start.go
index 6832f3f4af..6e661840c6 100644
--- a/clicommand/agent_start.go
+++ b/clicommand/agent_start.go
@@ -418,7 +418,7 @@ var AgentStartCommand = cli.Command{
 		cli.StringFlag{
 			Name:   "bootstrap-script",
 			Value:  "",
-			Usage:  "The command that is executed for bootstrapping a job, defaults to the exec-job sub-command of this binary",
+			Usage:  "[DEPRECATED] The command that is executed for bootstrapping a job, defaults to the exec-job sub-command of this binary",
 			EnvVar: "BUILDKITE_BOOTSTRAP_SCRIPT_PATH",
 		},
 		cli.StringFlag{
@@ -656,7 +656,7 @@ var AgentStartCommand = cli.Command{
 			cfg.NoPTY = true
 		}
 
-		// Set a useful default for the bootstrap script
+		// Set a useful default for the job exec script
 		if cfg.JobExecutorScript == "" {
 			exePath, err := os.Executable()
 			if err != nil {
diff --git a/clicommand/exec-job.go b/clicommand/exec-job.go
index 2b667ba46a..b91d8b885a 100644
--- a/clicommand/exec-job.go
+++ b/clicommand/exec-job.go
@@ -87,7 +87,8 @@ type ExecJobConfig struct {
 	Debug                        bool     `cli:"debug"`
 	Shell                        string   `cli:"shell"`
 	Experiments                  []string `cli:"experiment" normalize:"list"`
-	Phases                       []string `cli:"phases" normalize:"list"`
+	Phases                       []string `cli:"phases" normalize:"list" deprecated-and-renamed-to:"exec-phases"`
+	ExecPhases                   []string `cli:"exec-phases" normalize:"list"`
 	Profile                      string   `cli:"profile"`
 	CancelSignal                 string   `cli:"cancel-signal"`
 	RedactedVars                 []string `cli:"redacted-vars" normalize:"list"`
@@ -322,6 +323,11 @@ var execJobFlags = []cli.Flag{
 	},
 	cli.StringSliceFlag{
 		Name:   "phases",
+		Usage:  "[DEPRECATED] The specific phases to execute. The order they're defined is irrelevant.",
+		EnvVar: "BUILDKITE_BOOTSTRAP_PHASES",
+	},
+	cli.StringSliceFlag{
+		Name:   "exec-phases",
 		Usage:  "The specific phases to execute. The order they're defined is irrelevant.",
 		EnvVar: "BUILDKITE_BOOTSTRAP_PHASES",
 	},
@@ -509,16 +515,12 @@ func execJobAction(c *cli.Context) {
 	os.Exit(exitCode)
 }
 
-var (
-	BootstrapCommand = genBootstrap()
-	ExecJobCommand   = genExecJob()
-)
-
 func genBootstrap() cli.Command {
 	var help strings.Builder
 	help.WriteString("⚠️ ⚠️ ⚠️\n")
 	help.WriteString("DEPRECATED: Use `buildkite-agent exec-job` instead\n")
 	help.WriteString("⚠️ ⚠️ ⚠️\n\n")
+
 	err := execJobHelpTpl.Execute(&help, "bootstrap")
 	if err != nil {
 		// This can only hapen if we've mangled the template or its parsing
@@ -532,7 +534,13 @@ func genBootstrap() cli.Command {
 		Usage:       "[DEPRECATED] Run a Buildkite job locally",
 		Description: help.String(),
 		Flags:       execJobFlags,
-		Action:      execJobAction,
+		Action: func(c *cli.Context) {
+			fmt.Println("⚠️ WARNING ⚠️")
+			fmt.Println("This command (`buildkite-agent bootstrap`) is deprecated and will be removed in a future release")
+			fmt.Println("Please use `buildkite-agent exec-job` instead")
+			fmt.Println("")
+			execJobAction(c)
+		},
 	}
 }
 
@@ -551,12 +559,11 @@ func genExecJob() cli.Command {
 		Usage:       "Run a Buildkite job locally",
 		Description: help.String(),
 		Flags:       execJobFlags,
-		Action: func(c *cli.Context) {
-			fmt.Println("⚠️ WARNING ⚠️")
-			fmt.Println("This command (`buildkite-agent bootstrap`) is deprecated and will be removed in a future release")
-			fmt.Println("Please use `buildkite-agent exec-job` instead.")
-			fmt.Println("")
-			execJobAction(c)
-		},
+		Action:      execJobAction,
 	}
 }
+
+var (
+	BootstrapCommand = genBootstrap()
+	ExecJobCommand   = genExecJob()
+)
diff --git a/job/integration/executor_tester.go b/job/integration/executor_tester.go
index 0440653406..230a550e7b 100644
--- a/job/integration/executor_tester.go
+++ b/job/integration/executor_tester.go
@@ -263,7 +263,7 @@ func (b *ExecutorTester) Run(t *testing.T, env ...string) error {
 
 	buf := &buffer{}
 
-	if os.Getenv("DEBUG_BOOTSTRAP") == "1" {
+	if os.Getenv("DEBUG_JOB_EXEC") == "1" {
 		w := newTestLogWriter(t)
 		b.cmd.Stdout = io.MultiWriter(buf, w)
 		b.cmd.Stderr = io.MultiWriter(buf, w)