diff --git a/cmd/ipfs/init.go b/cmd/ipfs/init.go
index 4232cc262db4..0e5323683fa7 100644
--- a/cmd/ipfs/init.go
+++ b/cmd/ipfs/init.go
@@ -28,6 +28,7 @@ const (
 	algorithmDefault    = options.Ed25519Key
 	algorithmOptionName = "algorithm"
 	bitsOptionName      = "bits"
+	emptyRepoDefault    = true
 	emptyRepoOptionName = "empty-repo"
 	profileOptionName   = "profile"
 )
@@ -61,7 +62,7 @@ environment variable:
 	Options: []cmds.Option{
 		cmds.StringOption(algorithmOptionName, "a", "Cryptographic algorithm to use for key generation.").WithDefault(algorithmDefault),
 		cmds.IntOption(bitsOptionName, "b", "Number of bits to use in the generated RSA private key."),
-		cmds.BoolOption(emptyRepoOptionName, "e", "Don't add and pin help files to the local storage."),
+		cmds.BoolOption(emptyRepoOptionName, "e", "Don't add and pin help files to the local storage.").WithDefault(emptyRepoDefault),
 		cmds.StringOption(profileOptionName, "p", "Apply profile settings to config. Multiple profiles can be separated by ','"),
 
 		// TODO need to decide whether to expose the override as a file or a
diff --git a/test/cli/init_test.go b/test/cli/init_test.go
index 359856e6baea..a45ef05d5b35 100644
--- a/test/cli/init_test.go
+++ b/test/cli/init_test.go
@@ -33,9 +33,7 @@ func testInitAlgo(t *testing.T, initFlags []string, expOutputName string, expPee
 		lines := []string{
 			fmt.Sprintf("generating %s keypair...done", expOutputName),
 			fmt.Sprintf("peer identity: %s", node.PeerID().String()),
-			fmt.Sprintf("initializing IPFS node at %s", node.Dir),
-			"to get started, enter:",
-			fmt.Sprintf("\n\tipfs cat /ipfs/%s/readme\n\n", CIDWelcomeDocs),
+			fmt.Sprintf("initializing IPFS node at %s\n", node.Dir),
 		}
 		expectedInitOutput := strings.Join(lines, "\n")
 		assert.Equal(t, expectedInitOutput, initRes.Stdout.String())
@@ -54,26 +52,28 @@ func testInitAlgo(t *testing.T, initFlags []string, expOutputName string, expPee
 		res := node.IPFS("config", "Mounts.IPFS")
 		assert.Equal(t, "/ipfs", res.Stdout.Trimmed())
 
-		node.IPFS("cat", fmt.Sprintf("/ipfs/%s/readme", CIDWelcomeDocs))
+		catRes := node.RunIPFS("cat", fmt.Sprintf("/ipfs/%s/readme", CIDWelcomeDocs))
+		assert.NotEqual(t, 0, catRes.ExitErr.ExitCode(), "welcome readme doesn't exist")
 	})
 
-	t.Run("init empty repo", func(t *testing.T) {
+	t.Run("init without empty repo", func(t *testing.T) {
 		t.Parallel()
 		node := harness.NewT(t).NewNode()
-		initRes := node.IPFS(StrCat("init", "--empty-repo", initFlags)...)
+		initRes := node.IPFS(StrCat("init", "--empty-repo=false", initFlags)...)
 
 		validatePeerID(t, node.PeerID(), expPeerIDPubKeyErr, expPeerIDPubKeyType)
 
 		lines := []string{
 			fmt.Sprintf("generating %s keypair...done", expOutputName),
 			fmt.Sprintf("peer identity: %s", node.PeerID().String()),
-			fmt.Sprintf("initializing IPFS node at %s\n", node.Dir),
+			fmt.Sprintf("initializing IPFS node at %s", node.Dir),
+			"to get started, enter:",
+			fmt.Sprintf("\n\tipfs cat /ipfs/%s/readme\n\n", CIDWelcomeDocs),
 		}
 		expectedEmptyInitOutput := strings.Join(lines, "\n")
 		assert.Equal(t, expectedEmptyInitOutput, initRes.Stdout.String())
 
-		catRes := node.RunIPFS("cat", fmt.Sprintf("/ipfs/%s/readme", CIDWelcomeDocs))
-		assert.NotEqual(t, 0, catRes.ExitErr.ExitCode(), "welcome readme doesn't exist")
+		node.IPFS("cat", fmt.Sprintf("/ipfs/%s/readme", CIDWelcomeDocs))
 
 		idRes := node.IPFS("id", "-f", "<aver>")
 		version := node.IPFS("version", "-n").Stdout.Trimmed()
diff --git a/test/sharness/lib/test-lib.sh b/test/sharness/lib/test-lib.sh
index 1f1491f9ebf6..f135cdd7940e 100644
--- a/test/sharness/lib/test-lib.sh
+++ b/test/sharness/lib/test-lib.sh
@@ -194,7 +194,7 @@ test_config_set() {
 }
 
 test_init_ipfs() {
-
+  args=("$@")
 
   # we set the Addresses.API config variable.
   # the cli client knows to use it, so only need to set.
@@ -202,7 +202,7 @@ test_init_ipfs() {
 
   test_expect_success "ipfs init succeeds" '
     export IPFS_PATH="$(pwd)/.ipfs" &&
-    ipfs init --profile=test > /dev/null
+    ipfs init "${args[@]}" --profile=test > /dev/null
   '
 
   test_expect_success "prepare config -- mounting" '
diff --git a/test/sharness/t0025-datastores.sh b/test/sharness/t0025-datastores.sh
index ec99accb5e7e..f0ddd4e2e8fe 100755
--- a/test/sharness/t0025-datastores.sh
+++ b/test/sharness/t0025-datastores.sh
@@ -4,9 +4,9 @@ test_description="Test non-standard datastores"
 
 . lib/test-lib.sh
 
-test_expect_success "'ipfs init --profile=badgerds' succeeds" '
+test_expect_success "'ipfs init --empty-repo=false --profile=badgerds' succeeds" '
   BITS="2048" &&
-  ipfs init --profile=badgerds
+  ipfs init --empty-repo=false --profile=badgerds
 '
 
 test_expect_success "'ipfs pin ls' works" '
diff --git a/test/sharness/t0054-dag-car-import-export.sh b/test/sharness/t0054-dag-car-import-export.sh
index f378e9128e56..fe6f11476912 100755
--- a/test/sharness/t0054-dag-car-import-export.sh
+++ b/test/sharness/t0054-dag-car-import-export.sh
@@ -171,7 +171,7 @@ test_expect_success "shut down nodes" '
 
 
 # We want to just init the repo, without using a daemon for stuff below
-test_init_ipfs
+test_init_ipfs --empty-repo=false
 
 
 test_expect_success "basic offline export of 'getting started' dag works" '
diff --git a/test/sharness/t0080-repo.sh b/test/sharness/t0080-repo.sh
index 7bd84b276a7e..3f33a5f440b5 100755
--- a/test/sharness/t0080-repo.sh
+++ b/test/sharness/t0080-repo.sh
@@ -8,7 +8,7 @@ test_description="Test ipfs repo operations"
 
 . lib/test-lib.sh
 
-test_init_ipfs
+test_init_ipfs --empty-repo=false
 test_launch_ipfs_daemon_without_network
 
 test_expect_success "'ipfs repo gc' succeeds" '
diff --git a/test/sharness/t0100-name.sh b/test/sharness/t0100-name.sh
index 34f33ea4d89b..f49df341754e 100755
--- a/test/sharness/t0100-name.sh
+++ b/test/sharness/t0100-name.sh
@@ -15,13 +15,13 @@ test_name_with_self() {
         export IPFS_PATH="$(pwd)/.ipfs" &&
         case $SELF_ALG in
         default)
-                ipfs init --profile=test > /dev/null
+                ipfs init --empty-repo=false --profile=test > /dev/null
                 ;;
         rsa)
-                ipfs init --profile=test -a=rsa > /dev/null
+                ipfs init --empty-repo=false --profile=test -a=rsa > /dev/null
                 ;;
         ed25519)
-                ipfs init --profile=test -a=ed25519 > /dev/null
+                ipfs init --empty-repo=false --profile=test -a=ed25519 > /dev/null
                 ;;
         esac &&
         export PEERID=`ipfs key list --ipns-base=base36 -l | grep self | cut -d " " -f1` &&
@@ -273,7 +273,7 @@ test_name_with_key() {
 
         test_expect_success "ipfs init (key variant $GEN_ALG)" '
         export IPFS_PATH="$(pwd)/.ipfs" &&
-        ipfs init --profile=test > /dev/null
+        ipfs init --empty-repo=false --profile=test > /dev/null
         '
 
         test_expect_success "'prepare keys" '
@@ -317,7 +317,7 @@ test_name_with_key 'ed25519_b36'
 
 # `ipfs name inspect --verify` using the wrong RSA key should not succeed
 
-test_init_ipfs
+test_init_ipfs --empty-repo=false
 test_launch_ipfs_daemon
 
 test_expect_success "prepare RSA keys" '
diff --git a/test/sharness/t0600-issues-and-regressions-online.sh b/test/sharness/t0600-issues-and-regressions-online.sh
index 3468f23d6533..56384c0d02e5 100755
--- a/test/sharness/t0600-issues-and-regressions-online.sh
+++ b/test/sharness/t0600-issues-and-regressions-online.sh
@@ -4,7 +4,7 @@ test_description="Tests for various fixed issues and regressions."
 
 . lib/test-lib.sh
 
-test_init_ipfs
+test_init_ipfs --empty-repo=false
 
 test_launch_ipfs_daemon