diff --git a/.changelog/23560.txt b/.changelog/23560.txt
new file mode 100644
index 00000000000..e6c672b3485
--- /dev/null
+++ b/.changelog/23560.txt
@@ -0,0 +1,3 @@
+```release-note:bug
+api: Fixed bug where newlines in JobSubmission vars weren't encoded correctly
+```
diff --git a/api/jobs.go b/api/jobs.go
index 02c6b226da3..a0788f5176d 100644
--- a/api/jobs.go
+++ b/api/jobs.go
@@ -12,6 +12,7 @@ import (
 	"net/url"
 	"sort"
 	"strconv"
+	"strings"
 	"time"
 
 	"github.com/hashicorp/cronexpr"
@@ -997,6 +998,15 @@ func (js *JobSubmission) Canonicalize() {
 	if len(js.VariableFlags) == 0 {
 		js.VariableFlags = nil
 	}
+
+	// if there are multiline variables, make sure we escape the newline
+	// characters to preserve them. This way, when the job gets stopped and
+	// restarted in the UI, variable values will be parsed correctly.
+	for k, v := range js.VariableFlags {
+		if strings.Contains(v, "\n") {
+			js.VariableFlags[k] = strings.ReplaceAll(v, "\n", "\\n")
+		}
+	}
 }
 
 func (js *JobSubmission) Copy() *JobSubmission {
diff --git a/api/jobs_test.go b/api/jobs_test.go
index 2ab57479d9e..85873e959a6 100644
--- a/api/jobs_test.go
+++ b/api/jobs_test.go
@@ -1496,6 +1496,15 @@ func TestJobs_JobSubmission_Canonicalize(t *testing.T) {
 		js.Canonicalize()
 		must.Nil(t, js.VariableFlags)
 	})
+
+	t.Run("multiline var values", func(t *testing.T) {
+		js := &JobSubmission{
+			Source:        "abc123",
+			VariableFlags: map[string]string{"test": "foo\nbar"},
+		}
+		js.Canonicalize()
+		must.Eq(t, js.VariableFlags["test"], "foo\\nbar")
+	})
 }
 
 func TestJobs_JobSubmission_Copy(t *testing.T) {
diff --git a/command/agent/job_endpoint.go b/command/agent/job_endpoint.go
index b12427d9795..b9de05a9157 100644
--- a/command/agent/job_endpoint.go
+++ b/command/agent/job_endpoint.go
@@ -908,6 +908,8 @@ func apiJobSubmissionToStructs(submission *api.JobSubmission) *structs.JobSubmis
 	if submission == nil {
 		return nil
 	}
+
+	submission.Canonicalize()
 	return &structs.JobSubmission{
 		Source:        submission.Source,
 		Format:        submission.Format,