diff --git a/cmd/util/flags/configflags/ipfs.go b/cmd/util/flags/configflags/ipfs.go
index 044490beb3..0521732358 100644
--- a/cmd/util/flags/configflags/ipfs.go
+++ b/cmd/util/flags/configflags/ipfs.go
@@ -2,6 +2,9 @@ package configflags
 
 import "github.com/bacalhau-project/bacalhau/pkg/config/types"
 
+const ipfsEmbeddedDeprecationMessage = "The embedded IPFS node will be removed in a future version" +
+	"in favour of using --ipfs-connect and a self-hosted IPFS node"
+
 var IPFSFlags = []Definition{
 	{
 		FlagName:             "ipfs-swarm-addrs",
@@ -9,6 +12,8 @@ var IPFSFlags = []Definition{
 		DefaultValue:         Default.Node.IPFS.SwarmAddresses,
 		Description:          "IPFS multiaddress to connect the in-process IPFS node to - cannot be used with --ipfs-connect.",
 		EnvironmentVariables: []string{"BACALHAU_IPFS_SWARM_ADDRESSES"},
+		Deprecated:           true,
+		DeprecatedMessage:    ipfsEmbeddedDeprecationMessage,
 	},
 	{
 		FlagName:             "ipfs-swarm-key",
@@ -31,6 +36,8 @@ var IPFSFlags = []Definition{
 			"cannot be used with --ipfs-connect. " +
 			"Use \"--private-internal-ipfs=false\" to disable. " +
 			"To persist a local Ipfs node, set BACALHAU_SERVE_IPFS_PATH to a valid path.",
+		Deprecated:        true,
+		DeprecatedMessage: ipfsEmbeddedDeprecationMessage,
 	},
 	{
 		FlagName:             "ipfs-serve-path",
@@ -38,29 +45,39 @@ var IPFSFlags = []Definition{
 		DefaultValue:         Default.Node.IPFS.ServePath,
 		Description:          "path local Ipfs node will persist data to",
 		EnvironmentVariables: []string{"BACALHAU_SERVE_IPFS_PATH"},
+		Deprecated:           true,
+		DeprecatedMessage:    ipfsEmbeddedDeprecationMessage,
 	},
 	{
-		FlagName:     "ipfs-profile",
-		ConfigPath:   types.NodeIPFSProfile,
-		DefaultValue: Default.Node.IPFS.Profile,
-		Description:  "profile for internal IPFS node",
+		FlagName:          "ipfs-profile",
+		ConfigPath:        types.NodeIPFSProfile,
+		DefaultValue:      Default.Node.IPFS.Profile,
+		Description:       "profile for internal IPFS node",
+		Deprecated:        true,
+		DeprecatedMessage: ipfsEmbeddedDeprecationMessage,
 	},
 	{
-		FlagName:     "ipfs-swarm-listen-addresses",
-		ConfigPath:   types.NodeIPFSSwarmListenAddresses,
-		DefaultValue: Default.Node.IPFS.SwarmListenAddresses,
-		Description:  "addresses the internal IPFS node will listen on for swarm connections",
+		FlagName:          "ipfs-swarm-listen-addresses",
+		ConfigPath:        types.NodeIPFSSwarmListenAddresses,
+		DefaultValue:      Default.Node.IPFS.SwarmListenAddresses,
+		Description:       "addresses the internal IPFS node will listen on for swarm connections",
+		Deprecated:        true,
+		DeprecatedMessage: ipfsEmbeddedDeprecationMessage,
 	},
 	{
-		FlagName:     "ipfs-gateway-listen-addresses",
-		ConfigPath:   types.NodeIPFSGatewayListenAddresses,
-		DefaultValue: Default.Node.IPFS.GatewayListenAddresses,
-		Description:  "addresses the internal IPFS node will listen on for gateway connections",
+		FlagName:          "ipfs-gateway-listen-addresses",
+		ConfigPath:        types.NodeIPFSGatewayListenAddresses,
+		DefaultValue:      Default.Node.IPFS.GatewayListenAddresses,
+		Description:       "addresses the internal IPFS node will listen on for gateway connections",
+		Deprecated:        true,
+		DeprecatedMessage: ipfsEmbeddedDeprecationMessage,
 	},
 	{
-		FlagName:     "ipfs-api-listen-addresses",
-		ConfigPath:   types.NodeIPFSAPIListenAddresses,
-		DefaultValue: Default.Node.IPFS.APIListenAddresses,
-		Description:  "addresses the internal IPFS node will listen on for API connections",
+		FlagName:          "ipfs-api-listen-addresses",
+		ConfigPath:        types.NodeIPFSAPIListenAddresses,
+		DefaultValue:      Default.Node.IPFS.APIListenAddresses,
+		Description:       "addresses the internal IPFS node will listen on for API connections",
+		Deprecated:        true,
+		DeprecatedMessage: ipfsEmbeddedDeprecationMessage,
 	},
 }
diff --git a/cmd/util/flags/configflags/register.go b/cmd/util/flags/configflags/register.go
index cdbf09c8f1..de5c33e4c7 100644
--- a/cmd/util/flags/configflags/register.go
+++ b/cmd/util/flags/configflags/register.go
@@ -37,6 +37,8 @@ type Definition struct {
 	DefaultValue         interface{}
 	Description          string
 	EnvironmentVariables []string
+	Deprecated           bool
+	DeprecatedMessage    string
 }
 
 // BindFlags binds flags from a command to Viper using the provided definitions.
@@ -47,7 +49,7 @@ func BindFlags(cmd *cobra.Command, register map[string][]Definition) error {
 			// set the default value
 			viper.SetDefault(def.ConfigPath, def.DefaultValue)
 
-			// bind the flag to viper
+			// Bind the flag to viper
 			if err := viper.BindPFlag(def.ConfigPath, cmd.Flags().Lookup(def.FlagName)); err != nil {
 				return err
 			}
@@ -107,6 +109,11 @@ func RegisterFlags(cmd *cobra.Command, register map[string][]Definition) error {
 			default:
 				return fmt.Errorf("unhandled type: %T for flag %s", v, def.FlagName)
 			}
+
+			if def.Deprecated {
+				flag := fset.Lookup(def.FlagName)
+				flag.Deprecated = def.DeprecatedMessage
+			}
 		}
 		cmd.PersistentFlags().AddFlagSet(fset)
 	}