diff --git a/go.mod b/go.mod
index 0c100d9775..71473b38be 100644
--- a/go.mod
+++ b/go.mod
@@ -74,7 +74,7 @@ require (
 	github.com/spf13/pflag v1.0.9
 	github.com/spf13/viper v1.20.1
 	github.com/stretchr/testify v1.11.1
-	github.com/superfly/fly-go v0.2.3
+	github.com/superfly/fly-go v0.3.0
 	github.com/superfly/graphql v0.2.6
 	github.com/superfly/lfsc-go v0.1.1
 	github.com/superfly/macaroon v0.3.0
diff --git a/go.sum b/go.sum
index 2cf888a295..f4a42d36ee 100644
--- a/go.sum
+++ b/go.sum
@@ -637,8 +637,8 @@ github.com/stretchr/testify v1.11.1 h1:7s2iGBzp5EwR7/aIZr8ao5+dra3wiQyKjjFuvgVKu
 github.com/stretchr/testify v1.11.1/go.mod h1:wZwfW3scLgRK+23gO65QZefKpKQRnfz6sD981Nm4B6U=
 github.com/subosito/gotenv v1.6.0 h1:9NlTDc1FTs4qu0DDq7AEtTPNw6SVm7uBMsUCUjABIf8=
 github.com/subosito/gotenv v1.6.0/go.mod h1:Dk4QP5c2W3ibzajGcXpNraDfq2IrhjMIvMSWPKKo0FU=
-github.com/superfly/fly-go v0.2.3 h1:sK9lLjKNB/HWYtDcXp4G8WH4BIPkZe/8/MPa7VN1FzY=
-github.com/superfly/fly-go v0.2.3/go.mod h1:2gCFoNR3iUELADGTJtbBoviMa2jlh2vlPK3cKUajOp8=
+github.com/superfly/fly-go v0.3.0 h1:opzCfB5GeDe2AaqZgtPzWps+fW1zAMhISWAyQrhnV+Y=
+github.com/superfly/fly-go v0.3.0/go.mod h1:2gCFoNR3iUELADGTJtbBoviMa2jlh2vlPK3cKUajOp8=
 github.com/superfly/graphql v0.2.6 h1:zppbodNerWecoXEdjkhrqaNaSjGqobhXNlViHFuZzb4=
 github.com/superfly/graphql v0.2.6/go.mod h1:CVfDl31srm8HnJ9udwLu6hFNUW/P6GUM2dKcG1YQ8jc=
 github.com/superfly/lfsc-go v0.1.1 h1:dGjLgt81D09cG+aR9lJZIdmonjZSR5zYCi7s54+ZU2Q=
diff --git a/internal/command/machine/run.go b/internal/command/machine/run.go
index 861a5f5dec..915c3381cf 100644
--- a/internal/command/machine/run.go
+++ b/internal/command/machine/run.go
@@ -154,9 +154,13 @@ var sharedFlags = flag.Set{
 		Name:        "rootfs-persist",
 		Description: "Whether to persist the root filesystem across restarts. Options include 'never', 'always', and 'restart'.",
 	},
-	flag.Int{
+	flag.String{
 		Name:        "rootfs-size",
-		Description: "Root filesystem size in GB. Uses an overlayfs to allow the root filesystem to exceed its default size.",
+		Description: "Root filesystem size in GB. Accepts a plain number (in GB) or a human-readable size (e.g. 2gb, 5gb). Uses an overlayfs to allow the root filesystem to exceed its default size. Set to 0 to unset.",
+	},
+	flag.String{
+		Name:        "rootfs-fs-size",
+		Description: "Root filesystem size in GB. Accepts a plain number (in GB) or a human-readable size (e.g. 2gb, 5gb). Sets the size of the filesystem itself, independent of the rootfs volume size. Set to 0 to unset.",
 	},
 	flag.String{
 		Name:        "swap-size",
@@ -712,7 +716,7 @@ func determineMachineConfig(
 	}
 
 	// Root filesystem persistence and size
-	if flag.IsSpecified(ctx, "rootfs-persist") || flag.IsSpecified(ctx, "rootfs-size") {
+	if flag.IsSpecified(ctx, "rootfs-persist") || flag.IsSpecified(ctx, "rootfs-size") || flag.IsSpecified(ctx, "rootfs-fs-size") {
 		if machineConf.Rootfs == nil {
 			machineConf.Rootfs = &fly.MachineRootfs{}
 		}
@@ -731,11 +735,33 @@ func determineMachineConfig(
 		}
 
 		if flag.IsSpecified(ctx, "rootfs-size") {
-			size := flag.GetInt(ctx, "rootfs-size")
-			if size <= 0 {
-				return machineConf, fmt.Errorf("--rootfs-size must be greater than zero")
+			sizeGB, err := helpers.ParseSize(flag.GetString(ctx, "rootfs-size"), units.RAMInBytes, units.GiB)
+			if err != nil {
+				return machineConf, fmt.Errorf("invalid rootfs size: %w", err)
+			}
+			if sizeGB < 0 {
+				return machineConf, fmt.Errorf("--rootfs-size must not be negative")
+			}
+			machineConf.Rootfs.SizeGB = uint64(sizeGB)
+		}
+
+		if flag.IsSpecified(ctx, "rootfs-fs-size") {
+			sizeGB, err := helpers.ParseSize(flag.GetString(ctx, "rootfs-fs-size"), units.RAMInBytes, units.GiB)
+			if err != nil {
+				return machineConf, fmt.Errorf("invalid rootfs fs size: %w", err)
+			}
+			if sizeGB < 0 {
+				return machineConf, fmt.Errorf("--rootfs-fs-size must not be negative")
+			}
+			machineConf.Rootfs.FsSizeGB = uint64(sizeGB)
+		}
+
+		if machineConf.Rootfs.FsSizeGB > 0 {
+			if machineConf.Rootfs.SizeGB == 0 {
+				machineConf.Rootfs.SizeGB = machineConf.Rootfs.FsSizeGB
+			} else if machineConf.Rootfs.FsSizeGB > machineConf.Rootfs.SizeGB {
+				return machineConf, fmt.Errorf("--rootfs-fs-size must be smaller than or equal to --rootfs-size")
 			}
-			machineConf.Rootfs.SizeGB = uint64(size)
 		}
 	}
 
diff --git a/test/preflight/fly_machine_test.go b/test/preflight/fly_machine_test.go
index 86d7732099..1c35ba3327 100644
--- a/test/preflight/fly_machine_test.go
+++ b/test/preflight/fly_machine_test.go
@@ -127,6 +127,53 @@ func TestFlyMachineRun_standbyFor(t *testing.T) {
 	require.Equal(f, []string{s1.ID}, s2.Config.Standbys)
 }
 
+// test --rootfs-size and --rootfs-fs-size flags
+func TestFlyMachineRun_rootfsSize(t *testing.T) {
+	f := testlib.NewTestEnvFromEnv(t)
+	appName := f.CreateRandomAppMachines()
+
+	// Run with --rootfs-size only
+	f.Fly("machine run -a %s nginx --rootfs-size 5 --region %s", appName, f.PrimaryRegion())
+	ml := f.MachinesList(appName)
+	require.Equal(f, 1, len(ml))
+	m := ml[0]
+	require.NotNil(f, m.Config.Rootfs)
+	require.Equal(f, uint64(5), m.Config.Rootfs.SizeGB)
+	require.Equal(f, uint64(0), m.Config.Rootfs.FsSizeGB)
+
+	// Update with --rootfs-fs-size, must be <= rootfs-size
+	f.Fly("machine update -a %s %s --rootfs-fs-size 3 -y", appName, m.ID)
+	m = f.MachinesList(appName)[0]
+	require.NotNil(f, m.Config.Rootfs)
+	require.Equal(f, uint64(5), m.Config.Rootfs.SizeGB)
+	require.Equal(f, uint64(3), m.Config.Rootfs.FsSizeGB)
+
+	// Update with human-readable size
+	f.Fly("machine update -a %s %s --rootfs-size 10gb -y", appName, m.ID)
+	m = f.MachinesList(appName)[0]
+	require.NotNil(f, m.Config.Rootfs)
+	require.Equal(f, uint64(10), m.Config.Rootfs.SizeGB)
+
+	// Run with --rootfs-fs-size only, should default rootfs-size to match
+	f.Fly("machine run -a %s nginx --rootfs-fs-size 4 --region %s", appName, f.PrimaryRegion())
+	ml = f.MachinesList(appName)
+	require.Equal(f, 2, len(ml))
+	m = ml[1]
+	require.NotNil(f, m.Config.Rootfs)
+	require.Equal(f, uint64(4), m.Config.Rootfs.SizeGB)
+	require.Equal(f, uint64(4), m.Config.Rootfs.FsSizeGB)
+
+	// Unset rootfs-fs-size by passing 0
+	f.Fly("machine update -a %s %s --rootfs-fs-size 0 -y", appName, m.ID)
+	m = f.MachinesList(appName)[1]
+	require.NotNil(f, m.Config.Rootfs)
+	require.Equal(f, uint64(0), m.Config.Rootfs.FsSizeGB)
+
+	// Error: rootfs-fs-size > rootfs-size
+	result := f.FlyAllowExitFailure("machine run -a %s nginx --rootfs-size 2 --rootfs-fs-size 5 --region %s", appName, f.PrimaryRegion())
+	require.NotEqual(f, 0, result.ExitCode())
+}
+
 // test --port (add, update, remove services and ports)
 func TestFlyMachineRun_port(t *testing.T) {
 	f := testlib.NewTestEnvFromEnv(t)