diff --git a/git/client.go b/git/client.go
index 908ee8c4f33..43568839afa 100644
--- a/git/client.go
+++ b/git/client.go
@@ -20,6 +20,9 @@ import (
 	"github.com/cli/safeexec"
 )
 
+// MergeBaseConfig is the configuration setting to keep track of the PR target branch.
+const MergeBaseConfig = "gh-merge-base"
+
 var remoteRE = regexp.MustCompile(`(.+)\s+(.+)\s+\((push|fetch)\)`)
 
 // This regexp exists to match lines of the following form:
@@ -376,7 +379,7 @@ func (c *Client) lookupCommit(ctx context.Context, sha, format string) ([]byte,
 // ReadBranchConfig parses the `branch.BRANCH.(remote|merge)` part of git config.
 func (c *Client) ReadBranchConfig(ctx context.Context, branch string) (cfg BranchConfig) {
 	prefix := regexp.QuoteMeta(fmt.Sprintf("branch.%s.", branch))
-	args := []string{"config", "--get-regexp", fmt.Sprintf("^%s(remote|merge|gh-merge-base)$", prefix)}
+	args := []string{"config", "--get-regexp", fmt.Sprintf("^%s(remote|merge|%s)$", prefix, MergeBaseConfig)}
 	cmd, err := c.Command(ctx, args...)
 	if err != nil {
 		return
@@ -406,13 +409,26 @@ func (c *Client) ReadBranchConfig(ctx context.Context, branch string) (cfg Branc
 			}
 		case "merge":
 			cfg.MergeRef = parts[1]
-		case "gh-merge-base":
+		case MergeBaseConfig:
 			cfg.MergeBase = parts[1]
 		}
 	}
 	return
 }
 
+// SetBranchConfig sets the named value on the given branch.
+func (c *Client) SetBranchConfig(ctx context.Context, branch, name, value string) error {
+	name = fmt.Sprintf("branch.%s.%s", branch, name)
+	args := []string{"config", name, value}
+	cmd, err := c.Command(ctx, args...)
+	if err != nil {
+		return err
+	}
+	// No output expected but check for any printed git error.
+	_, err = cmd.Output()
+	return err
+}
+
 func (c *Client) DeleteLocalTag(ctx context.Context, tag string) error {
 	args := []string{"tag", "-d", tag}
 	cmd, err := c.Command(ctx, args...)
diff --git a/pkg/cmd/issue/develop/develop.go b/pkg/cmd/issue/develop/develop.go
index fa01a3dacbf..bbffa60acea 100644
--- a/pkg/cmd/issue/develop/develop.go
+++ b/pkg/cmd/issue/develop/develop.go
@@ -171,6 +171,14 @@ func developRunCreate(opts *DevelopOptions, apiClient *api.Client, issueRepo ghr
 		return err
 	}
 
+	// Remember which branch to target when creating a PR.
+	if opts.BaseBranch != "" {
+		err = opts.GitClient.SetBranchConfig(ctx.Background(), branchName, git.MergeBaseConfig, opts.BaseBranch)
+		if err != nil {
+			return err
+		}
+	}
+
 	fmt.Fprintf(opts.IO.Out, "%s/%s/tree/%s\n", branchRepo.RepoHost(), ghrepo.FullName(branchRepo), branchName)
 
 	return checkoutBranch(opts, branchRepo, branchName)
diff --git a/pkg/cmd/issue/develop/develop_test.go b/pkg/cmd/issue/develop/develop_test.go
index abdebf0c8e9..831f03fc3bd 100644
--- a/pkg/cmd/issue/develop/develop_test.go
+++ b/pkg/cmd/issue/develop/develop_test.go
@@ -399,6 +399,7 @@ func TestDevelopRun(t *testing.T) {
 			},
 			runStubs: func(cs *run.CommandStubber) {
 				cs.Register(`git fetch origin \+refs/heads/my-branch:refs/remotes/origin/my-branch`, 0, "")
+				cs.Register(`git config branch\.my-branch\.gh-merge-base main`, 0, "")
 			},
 			expectedOut: "github.com/OWNER/REPO/tree/my-branch\n",
 		},