diff --git a/agent/config/builder.go b/agent/config/builder.go
index f1d787ebc7..919f2fdbb2 100644
--- a/agent/config/builder.go
+++ b/agent/config/builder.go
@@ -108,7 +108,7 @@ func NewBuilder(opts BuilderOpts) (*Builder, error) {
 	slices, values := b.splitSlicesAndValues(opts.Config)
 	b.Head = append(b.Head, newSource("flags.slices", slices))
 	for _, path := range opts.ConfigFiles {
-		sources, err := sourcesFromPath(path, opts)
+		sources, err := b.sourcesFromPath(path, opts.ConfigFormat)
 		if err != nil {
 			return nil, err
 		}
@@ -132,7 +132,7 @@ func NewBuilder(opts BuilderOpts) (*Builder, error) {
 // sourcesFromPath reads a single config file or all files in a directory (but
 // not its sub-directories) and returns Sources created from the
 // files.
-func sourcesFromPath(path string, options BuilderOpts) ([]Source, error) {
+func (b *Builder) sourcesFromPath(path string, format string) ([]Source, error) {
 	f, err := os.Open(path)
 	if err != nil {
 		return nil, fmt.Errorf("config: Open failed on %s. %s", path, err)
@@ -145,12 +145,12 @@ func sourcesFromPath(path string, options BuilderOpts) ([]Source, error) {
 	}
 
 	if !fi.IsDir() {
-		if !shouldParseFile(path, options.ConfigFormat) {
-			// TODO: log warning
+		if !shouldParseFile(path, format) {
+			b.warn("skipping file %v, extension must be .hcl or .json, or config format must be set", path)
 			return nil, nil
 		}
 
-		src, err := newSourceFromFile(path, options.ConfigFormat)
+		src, err := newSourceFromFile(path, format)
 		if err != nil {
 			return nil, err
 		}
@@ -185,11 +185,11 @@ func sourcesFromPath(path string, options BuilderOpts) ([]Source, error) {
 			continue
 		}
 
-		if !shouldParseFile(fp, options.ConfigFormat) {
-			// TODO: log warning
+		if !shouldParseFile(fp, format) {
+			b.warn("skipping file %v, extension must be .hcl or .json, or config format must be set", fp)
 			continue
 		}
-		src, err := newSourceFromFile(fp, options.ConfigFormat)
+		src, err := newSourceFromFile(fp, format)
 		if err != nil {
 			return nil, err
 		}
@@ -251,9 +251,6 @@ func (b *Builder) BuildAndValidate() (RuntimeConfig, error) {
 // warnings can still contain deprecation or format warnings that should
 // be presented to the user.
 func (b *Builder) Build() (rt RuntimeConfig, err error) {
-	b.err = nil
-	b.Warnings = nil
-
 	// TODO: move to NewBuilder to remove Builder.options field
 	configFormat := b.options.ConfigFormat
 	if configFormat != "" && configFormat != "json" && configFormat != "hcl" {
diff --git a/agent/config/builder_test.go b/agent/config/builder_test.go
index aa6cec17f4..a2eddaf75d 100644
--- a/agent/config/builder_test.go
+++ b/agent/config/builder_test.go
@@ -44,6 +44,7 @@ func TestNewBuilder_PopulatesSourcesFromConfigFiles(t *testing.T) {
 		{Name: filepath.Join(paths[3], "b.json"), Format: "json", Data: "content b"},
 	}
 	require.Equal(t, expected, b.Sources)
+	require.Len(t, b.Warnings, 2)
 }
 
 func TestNewBuilder_PopulatesSourcesFromConfigFiles_WithConfigFormat(t *testing.T) {
diff --git a/agent/config/runtime_test.go b/agent/config/runtime_test.go
index 2598946bb3..424f87afce 100644
--- a/agent/config/runtime_test.go
+++ b/agent/config/runtime_test.go
@@ -451,6 +451,9 @@ func TestConfigFlagsAndEdgecases(t *testing.T) {
 				writeFile(filepath.Join(dataDir, "conf", "valid.json"), []byte(`{"datacenter":"a"}`))
 				writeFile(filepath.Join(dataDir, "conf", "invalid.skip"), []byte(`NOPE`))
 			},
+			warns: []string{
+				"skipping file " + filepath.Join(dataDir, "conf", "invalid.skip") + ", extension must be .hcl or .json, or config format must be set",
+			},
 		},
 		{
 			desc: "-config-format=json",
@@ -6002,6 +6005,7 @@ func TestFullConfig(t *testing.T) {
 			if err := fs.Parse(flagSrc); err != nil {
 				t.Fatalf("ParseFlags: %s", err)
 			}
+			require.Len(t, fs.Args(), 0)
 
 			b, err := NewBuilder(flags)
 			if err != nil {
diff --git a/command/services/config.go b/command/services/config.go
index 94b026ff5b..677757da39 100644
--- a/command/services/config.go
+++ b/command/services/config.go
@@ -7,12 +7,13 @@ import (
 	"github.com/hashicorp/consul/agent/config"
 	"github.com/hashicorp/consul/agent/structs"
 	"github.com/hashicorp/consul/api"
+	"github.com/mitchellh/cli"
 	"github.com/mitchellh/mapstructure"
 )
 
 // ServicesFromFiles returns the list of agent service registration structs
 // from a set of file arguments.
-func ServicesFromFiles(files []string) ([]*api.AgentServiceRegistration, error) {
+func ServicesFromFiles(ui cli.Ui, files []string) ([]*api.AgentServiceRegistration, error) {
 	// We set devMode to true so we can get the basic valid default
 	// configuration. devMode doesn't set any services by default so this
 	// is okay since we only look at services.
@@ -29,6 +30,9 @@ func ServicesFromFiles(files []string) ([]*api.AgentServiceRegistration, error)
 	if err != nil {
 		return nil, err
 	}
+	for _, w := range b.Warnings {
+		ui.Warn(w)
+	}
 
 	// The services are now in "structs.ServiceDefinition" form and we need
 	// them in "api.AgentServiceRegistration" form so do the conversion.
diff --git a/command/services/deregister/deregister.go b/command/services/deregister/deregister.go
index fc8efedd09..2cae8172a6 100644
--- a/command/services/deregister/deregister.go
+++ b/command/services/deregister/deregister.go
@@ -55,7 +55,7 @@ func (c *cmd) Run(args []string) int {
 		ID: c.flagId}}
 	if len(args) > 0 {
 		var err error
-		svcs, err = services.ServicesFromFiles(args)
+		svcs, err = services.ServicesFromFiles(c.UI, args)
 		if err != nil {
 			c.UI.Error(fmt.Sprintf("Error: %s", err))
 			return 1
diff --git a/command/services/register/register.go b/command/services/register/register.go
index 96835de09a..52f030edb2 100644
--- a/command/services/register/register.go
+++ b/command/services/register/register.go
@@ -103,7 +103,7 @@ func (c *cmd) Run(args []string) int {
 
 	if len(args) > 0 {
 		var err error
-		svcs, err = services.ServicesFromFiles(args)
+		svcs, err = services.ServicesFromFiles(c.UI, args)
 		if err != nil {
 			c.UI.Error(fmt.Sprintf("Error: %s", err))
 			return 1
diff --git a/command/validate/validate.go b/command/validate/validate.go
index fb3d55f475..754f0e5ded 100644
--- a/command/validate/validate.go
+++ b/command/validate/validate.go
@@ -61,6 +61,9 @@ func (c *cmd) Run(args []string) int {
 		return 1
 	}
 	if !c.quiet {
+		for _, w := range b.Warnings {
+			c.UI.Warn(w)
+		}
 		c.UI.Output("Configuration is valid!")
 	}
 	return 0