diff --git a/plugins/pass/commands/run.go b/plugins/pass/commands/run.go
index 85474dfc..42546e5f 100644
--- a/plugins/pass/commands/run.go
+++ b/plugins/pass/commands/run.go
@@ -53,6 +53,7 @@ var runLong string
 type runOpts struct {
 	clientOpts
 	envFiles []string
+	env      []string
 }
 
 // RunCommand uses [api.DesktopSocketPath] by default.
@@ -72,7 +73,7 @@ func newRunCommand(opts runOpts) *cobra.Command {
 		Example: strings.Trim(runExample, "\n"),
 		Args:    cobra.MinimumNArgs(1),
 		RunE: func(cmd *cobra.Command, args []string) error {
-			merged, err := mergeEnv(os.Environ(), opts.envFiles)
+			merged, err := mergeEnv(os.Environ(), opts.envFiles, opts.env)
 			if err != nil {
 				return err
 			}
@@ -147,10 +148,12 @@ func newRunCommand(opts runOpts) *cobra.Command {
 	}
 	cmd.Flags().StringArrayVar(&opts.envFiles, "env-file", nil,
 		"Read environment variables from a dotenv-formatted file. Repeatable; later files override earlier files and the process environment.")
+	cmd.Flags().StringArrayVarP(&opts.env, "env", "e", nil,
+		"Set an environment variable as `KEY=VALUE`; the value may be an se:// reference. Repeatable; overrides --env-file and the process environment.")
 	return cmd
 }
 
-func mergeEnv(processEnv, files []string) ([]string, error) {
+func mergeEnv(processEnv, files, env []string) ([]string, error) {
 	merged := make(map[string]string, len(processEnv))
 	for _, kv := range processEnv {
 		if k, v, ok := strings.Cut(kv, "="); ok {
@@ -164,6 +167,13 @@ func mergeEnv(processEnv, files []string) ([]string, error) {
 		}
 		maps.Copy(merged, parsed)
 	}
+	for _, kv := range env {
+		k, v, ok := strings.Cut(kv, "=")
+		if !ok || k == "" {
+			return nil, fmt.Errorf("invalid --env %q: expected KEY=VALUE", kv)
+		}
+		merged[k] = v
+	}
 	out := make([]string, 0, len(merged))
 	for k, v := range merged {
 		out = append(out, k+"="+v)
diff --git a/plugins/pass/commands/run_example.md b/plugins/pass/commands/run_example.md
index 414b0134..21519d4a 100644
--- a/plugins/pass/commands/run_example.md
+++ b/plugins/pass/commands/run_example.md
@@ -1,29 +1,41 @@
 ### Run a command with one secret in its environment:
 
 ```console
-$ SE_TOKEN=se://gh-token docker pass run -- gh repo list
+$ docker pass run -e GH_TOKEN=se://gh-token -- gh repo list
 ```
 
-### Multiple references:
+### Pass several secrets to a shell script, which reads them like any other variable:
 
 ```console
-$ DB_PASSWORD=se://myapp/postgres/password API_KEY=se://myapp/anthropic/api-key docker pass run -- ./my-binary
+$ docker pass run -e DB_PASSWORD=se://myapp/password -e API_KEY=se://myapp/api-key -- ./deploy.sh
+```
+
+### Resolve references from a dotenv file:
+
+```console
+$ docker pass run --env-file .env -- ./deploy.sh
+```
+
+### Inline shell (single quotes leave `$DB_PASSWORD` for the child shell to expand):
+
+```console
+$ docker pass run -e DB_PASSWORD=se://myapp/password -- sh -c 'pg_dump "postgres://app:$DB_PASSWORD@db/app" > backup.sql'
 ```
 
 ### Wildcard pattern (the first matching secret is used):
 
 ```console
-$ DB_PASSWORD=se://*/postgres/password docker pass run -- ./my-binary
+$ docker pass run -e DB_PASSWORD=se://*/password -- ./deploy.sh
 ```
 
-### Resolve references from a dotenv file:
+### References already in the calling environment are resolved too:
 
 ```console
-$ docker pass run --env-file .env -- ./my-binary
+$ GH_TOKEN=se://gh-token docker pass run -- gh repo list
 ```
 
-### Multiple files (later overrides earlier; files override the process environment):
+### Combine sources (`--env` overrides `--env-file`; later files override earlier ones; all override the process environment):
 
 ```console
-$ docker pass run --env-file .env --env-file .env.local -- ./my-binary
+$ docker pass run --env-file .env --env-file .env.local -e DB_PASSWORD=se://myapp/postgres/password -- ./deploy.sh
 ```
diff --git a/plugins/pass/commands/run_long.md b/plugins/pass/commands/run_long.md
index ef8209b5..3fbf0496 100644
--- a/plugins/pass/commands/run_long.md
+++ b/plugins/pass/commands/run_long.md
@@ -1,7 +1,8 @@
-Scans the current environment (plus any `--env-file` inputs) for variables
-whose value is exactly `se://<ID|pattern>`. Each reference is resolved through the
-secrets-engine daemon and the resolved value is passed to the child process.
-When several secrets match, the first match is used.
+Scans the current environment (plus any `--env-file` and `--env` inputs) for
+variables whose value is exactly `se://<ID|pattern>`. Each reference is resolved
+through the secrets-engine daemon and the resolved value is passed to the child
+process. When several secrets match, the first match is used.
+`--env` overrides `--env-file`; both override the process environment.
 The child inherits stdin, stdout, and stderr.
 
 Requires the secrets-engine daemon (Docker Desktop) to be running.
diff --git a/plugins/pass/commands/run_test.go b/plugins/pass/commands/run_test.go
index a4215095..22f6cbbc 100644
--- a/plugins/pass/commands/run_test.go
+++ b/plugins/pass/commands/run_test.go
@@ -249,14 +249,14 @@ func TestMergeEnv(t *testing.T) {
 	t.Parallel()
 
 	t.Run("no files returns sorted process env", func(t *testing.T) {
-		out, err := mergeEnv([]string{"B=2", "A=1"}, nil)
+		out, err := mergeEnv([]string{"B=2", "A=1"}, nil, nil)
 		require.NoError(t, err)
 		assert.Equal(t, []string{"A=1", "B=2"}, out)
 	})
 
 	t.Run("file overrides process env", func(t *testing.T) {
 		f := writeEnvFile(t, "A=from-file\nC=new\n")
-		out, err := mergeEnv([]string{"A=from-process", "B=keep"}, []string{f})
+		out, err := mergeEnv([]string{"A=from-process", "B=keep"}, []string{f}, nil)
 		require.NoError(t, err)
 		assert.Equal(t, []string{"A=from-file", "B=keep", "C=new"}, out)
 	})
@@ -264,14 +264,14 @@ func TestMergeEnv(t *testing.T) {
 	t.Run("later file overrides earlier file", func(t *testing.T) {
 		f1 := writeEnvFile(t, "A=from-file-1\n")
 		f2 := writeEnvFile(t, "A=from-file-2\n")
-		out, err := mergeEnv(nil, []string{f1, f2})
+		out, err := mergeEnv(nil, []string{f1, f2}, nil)
 		require.NoError(t, err)
 		assert.Equal(t, []string{"A=from-file-2"}, out)
 	})
 
 	t.Run("comments and quoted values", func(t *testing.T) {
 		f := writeEnvFile(t, "# this is a comment\nGREETING=\"hello world\"\nQUOTED='no $expand'\n")
-		out, err := mergeEnv(nil, []string{f})
+		out, err := mergeEnv(nil, []string{f}, nil)
 		require.NoError(t, err)
 		assert.Equal(t, []string{
 			"GREETING=hello world",
@@ -281,17 +281,45 @@ func TestMergeEnv(t *testing.T) {
 
 	t.Run("missing file returns error and does not partially apply", func(t *testing.T) {
 		f := writeEnvFile(t, "A=present\n")
-		out, err := mergeEnv([]string{"B=keep"}, []string{f, "/does/not/exist/.env"})
+		out, err := mergeEnv([]string{"B=keep"}, []string{f, "/does/not/exist/.env"}, nil)
 		require.Error(t, err)
 		assert.Nil(t, out)
 		assert.Contains(t, err.Error(), "/does/not/exist/.env")
 	})
 
+	t.Run("--env overrides files and the process env", func(t *testing.T) {
+		f := writeEnvFile(t, "A=from-file\nB=from-file\n")
+		out, err := mergeEnv([]string{"A=from-process", "C=keep"}, []string{f}, []string{"A=from-flag", "D=new"})
+		require.NoError(t, err)
+		assert.Equal(t, []string{"A=from-flag", "B=from-file", "C=keep", "D=new"}, out)
+	})
+
+	t.Run("later --env overrides earlier --env", func(t *testing.T) {
+		out, err := mergeEnv(nil, nil, []string{"A=1", "A=2"})
+		require.NoError(t, err)
+		assert.Equal(t, []string{"A=2"}, out)
+	})
+
+	t.Run("--env splits at the first = and allows an empty value", func(t *testing.T) {
+		out, err := mergeEnv(nil, nil, []string{"CHECK=KEY=WANT", "EMPTY="})
+		require.NoError(t, err)
+		assert.Equal(t, []string{"CHECK=KEY=WANT", "EMPTY="}, out)
+	})
+
+	t.Run("--env without KEY=VALUE is rejected", func(t *testing.T) {
+		for _, bad := range []string{"NOVALUE", "=value", ""} {
+			out, err := mergeEnv([]string{"B=keep"}, nil, []string{bad})
+			require.Error(t, err, bad)
+			assert.Nil(t, out)
+			assert.ErrorContains(t, err, "expected KEY=VALUE")
+		}
+	})
+
 	t.Run("preserves se:// values for downstream parseEnv", func(t *testing.T) {
 		f := writeEnvFile(t, "SE_TOKEN=se://gh-token\nPLAIN=v\n")
-		out, err := mergeEnv(nil, []string{f})
+		out, err := mergeEnv(nil, []string{f}, []string{"PG_PWD=se://*/postgres/password"})
 		require.NoError(t, err)
-		assert.Equal(t, []string{"PLAIN=v", "SE_TOKEN=se://gh-token"}, out)
+		assert.Equal(t, []string{"PG_PWD=se://*/postgres/password", "PLAIN=v", "SE_TOKEN=se://gh-token"}, out)
 	})
 }
 
@@ -434,6 +462,41 @@ func TestRunCommand(t *testing.T) {
 		assert.Equal(t, []string{"authorize gh-token", "resolve gh-token"}, engine.recorded())
 	})
 
+	t.Run("resolves references set with --env", func(t *testing.T) {
+		engine := &mockEngine{allow: true, store: map[secrets.ID]string{
+			secrets.MustParseID("gh-token"): "ghp_abc123",
+		}}
+		// The env-file plants a dangling reference; --env must win over it.
+		envFile := writeEnvFile(t, "SE_TOKEN=se://does-not-exist\n")
+		cmd, err := RunCommand(WithTimeout(time.Second), WithSocketPath(engine.serve(t)))
+		require.NoError(t, err)
+		cmd.SetArgs([]string{
+			"--env-file", envFile,
+			"-e", "SE_TOKEN=se://gh-token",
+			"-e", helperActiveEnv + "=1",
+			"--env", helperCheckEnv + "=SE_TOKEN=ghp_abc123",
+			exe,
+		})
+		cmd.SetContext(t.Context())
+		cmd.SetOut(testWriter{t})
+		cmd.SetErr(testWriter{t})
+		require.NoError(t, cmd.Execute())
+		assert.Equal(t, []string{"authorize gh-token", "resolve gh-token"}, engine.recorded())
+	})
+
+	t.Run("a malformed --env fails before contacting the engine", func(t *testing.T) {
+		engine := &mockEngine{allow: true}
+		cmd, err := RunCommand(WithTimeout(time.Second), WithSocketPath(engine.serve(t)))
+		require.NoError(t, err)
+		cmd.SetArgs([]string{"-e", "NOVALUE", exe})
+		cmd.SetContext(t.Context())
+		cmd.SetOut(testWriter{t})
+		cmd.SetErr(testWriter{t})
+		err = cmd.Execute()
+		require.ErrorContains(t, err, `invalid --env "NOVALUE": expected KEY=VALUE`)
+		assert.Empty(t, engine.recorded())
+	})
+
 	t.Run("a denied authorization stops before resolving", func(t *testing.T) {
 		engine := &mockEngine{store: map[secrets.ID]string{
 			secrets.MustParseID("gh-token"): "ghp_abc123",