diff --git a/go.mod b/go.mod
index 4b03641..685748f 100644
--- a/go.mod
+++ b/go.mod
@@ -11,7 +11,7 @@ require (
 	github.com/santhosh-tekuri/jsonschema/v5 v5.0.0
 	github.com/spf13/cobra v1.1.3
 	github.com/stretchr/testify v1.9.0
-	golang.org/x/mod v0.12.0
+	golang.org/x/mod v0.19.0
 )
 
 require (
diff --git a/go.sum b/go.sum
index f978912..08aac65 100644
--- a/go.sum
+++ b/go.sum
@@ -605,8 +605,8 @@ golang.org/x/mod v0.4.0/go.mod h1:s0Qsj1ACt9ePp/hMypM3fl4fZqREWJwdYDEqhRiZZUA=
 golang.org/x/mod v0.4.1/go.mod h1:s0Qsj1ACt9ePp/hMypM3fl4fZqREWJwdYDEqhRiZZUA=
 golang.org/x/mod v0.6.0-dev.0.20220419223038-86c51ed26bb4/go.mod h1:jJ57K6gSWd91VN4djpZkiMVwK6gcyfeH4XE8wZrZaV4=
 golang.org/x/mod v0.8.0/go.mod h1:iBbtSCu2XBx23ZKBPSOrRkjjQPZFPuis4dIYUhu/chs=
-golang.org/x/mod v0.12.0 h1:rmsUpXtvNzj340zd98LZ4KntptpfRHwpFOHG188oHXc=
-golang.org/x/mod v0.12.0/go.mod h1:iBbtSCu2XBx23ZKBPSOrRkjjQPZFPuis4dIYUhu/chs=
+golang.org/x/mod v0.19.0 h1:fEdghXQSo20giMthA7cd28ZC+jts4amQ3YMXiP5oMQ8=
+golang.org/x/mod v0.19.0/go.mod h1:hTbmBsO62+eylJbnUtE2MGJUyE7QWk4xUqPFrRgJ+7c=
 golang.org/x/net v0.0.0-20180724234803-3673e40ba225/go.mod h1:mL1N/T3taQHkDXs73rZJwtUhF3w3ftmwwsq0BUmARs4=
 golang.org/x/net v0.0.0-20180826012351-8a410e7b638d/go.mod h1:mL1N/T3taQHkDXs73rZJwtUhF3w3ftmwwsq0BUmARs4=
 golang.org/x/net v0.0.0-20181023162649-9b4f9f5ad519/go.mod h1:mL1N/T3taQHkDXs73rZJwtUhF3w3ftmwwsq0BUmARs4=
diff --git a/plugin.go b/plugin.go
index c7e201a..d249751 100644
--- a/plugin.go
+++ b/plugin.go
@@ -8,20 +8,33 @@ import (
 	"github.com/krakendio/krakend-cobra/v2/plugin"
 	"github.com/spf13/cobra"
 	"golang.org/x/mod/modfile"
+	"golang.org/x/mod/module"
 )
 
-// indirectRequires returns the indirect dependencies of the go.sum file.
-func indirectRequires(goSum string) (map[string]struct{}, error) {
-	dir := filepath.Dir(goSum)
-	filename := filepath.Join(dir, "go.mod")
+const (
+	// goName is the name of the diff which represents the go version.
+	goName = "go"
+
+	// libcName is the name of the diff which represents the libc version.
+	libcName = "libc"
+)
+
+// goMod returns the go.mod file path from the go.sum file path.
+func goMod(goSum string) string {
+	return filepath.Join(filepath.Dir(goSum), "go.mod")
+}
+
+// indirectRequires returns the details and indirect dependencies of the go.sum file.
+func indirectRequires(goSum string) (*modfile.File, map[string]struct{}, error) {
+	filename := goMod(goSum)
 	data, err := os.ReadFile(filename)
 	if err != nil {
-		return nil, fmt.Errorf("reading go.mod: %w", err)
+		return nil, nil, fmt.Errorf("read go.mod: %w", err)
 	}
 
 	f, err := modfile.Parse(filename, data, nil)
 	if err != nil {
-		return nil, fmt.Errorf("parsing go.mod: %w", err)
+		return nil, nil, fmt.Errorf("parse go.mod: %w", err)
 	}
 
 	indirects := map[string]struct{}{}
@@ -31,7 +44,23 @@ func indirectRequires(goSum string) (map[string]struct{}, error) {
 		}
 	}
 
-	return indirects, nil
+	return f, indirects, nil
+}
+
+// writeModFile writes the modfile.File to the go.mod file determined from goSum.
+func writeModFile(goSum string, f *modfile.File) error {
+	f.Cleanup()
+	data, err := f.Format()
+	if err != nil {
+		return fmt.Errorf("format go.mod: %w", err)
+	}
+
+	filename := goMod(goSum)
+	if err = os.WriteFile(filename, data, 0644); err != nil {
+		return fmt.Errorf("write go.sum: %w", err)
+	}
+
+	return nil
 }
 
 // getBuildInfo returns the dependencies of the binary calling it.
@@ -66,32 +95,99 @@ func pluginFuncErr(cmd *cobra.Command, _ []string) error {
 		return nil
 	}
 
-	if gogetEnabled {
-		indirects, err := indirectRequires(goSum)
-		if err != nil {
+	var indirects map[string]struct{}
+	var modFile *modfile.File
+	if gogetEnabled || fixEnabled {
+		if modFile, indirects, err = indirectRequires(goSum); err != nil {
 			return err
 		}
-		for _, diff := range diffs {
-			if diff.Name != "go" && diff.Name != "libc" {
-				if _, ok := indirects[diff.Name]; ok {
-					cmd.Printf("go mod edit --replace %s=%s@%s\n", diff.Name, diff.Name, diff.Expected)
-				} else {
-					cmd.Printf("go get %s@%s\n", diff.Name, diff.Expected)
-				}
+	}
+
+	var fixed int
+	if !fixEnabled {
+		outputFixes(cmd, diffs, indirects)
+	} else if fixed, err = applyFixes(cmd, diffs, modFile, indirects); err != nil {
+		return err
+	}
+
+	// Report any remaining incompatibilities.
+	if len(diffs) != fixed {
+		if fixed > 0 {
+			return fmt.Errorf("%d incompatibilities fixed, %d left", fixed, len(diffs)-fixed)
+		}
+
+		return fmt.Errorf("%d incompatibilities found", len(diffs))
+	}
+
+	return nil
+}
+
+// outputFixes prints the incompatibilities.
+func outputFixes(cmd *cobra.Command, diffs []plugin.Diff, indirects map[string]struct{}) {
+	for _, diff := range diffs {
+		if diff.Name != goName && diff.Name != libcName && gogetEnabled {
+			if _, ok := indirects[diff.Name]; ok {
+				cmd.Printf("go mod edit --replace %s=%s@%s\n", diff.Name, diff.Name, diff.Expected)
+			} else {
+				cmd.Printf("go get %s@%s\n", diff.Name, diff.Expected)
+			}
+			continue
+		}
+
+		cmd.Println(diff.Name)
+		cmd.Println("\thave:", diff.Have)
+		cmd.Println("\twant:", diff.Expected)
+	}
+}
+
+// applyFixes applies the fixes and returns the number of incompatibilities fixed.
+func applyFixes(cmd *cobra.Command, diffs []plugin.Diff, modFile *modfile.File, indirects map[string]struct{}) (int, error) {
+	var replaces []plugin.Diff
+	var requires []*modfile.Require
+	for _, diff := range diffs {
+		if diff.Name != goName && diff.Name != libcName {
+			if _, ok := indirects[diff.Name]; ok {
+				replaces = append(replaces, diff)
 				continue
 			}
 
-			cmd.Println(diff.Name)
-			cmd.Println("\thave:", diff.Have)
-			cmd.Println("\twant:", diff.Expected)
+			requires = append(requires, &modfile.Require{
+				Mod: module.Version{
+					Path:    diff.Name,
+					Version: diff.Expected,
+				},
+			})
+			continue
 		}
-	} else {
-		for _, diff := range diffs {
-			cmd.Println(diff.Name)
-			cmd.Println("\thave:", diff.Have)
-			cmd.Println("\twant:", diff.Expected)
+
+		cmd.Println(diff.Name)
+		cmd.Println("\thave:", diff.Have)
+		cmd.Println("\twant:", diff.Expected)
+	}
+
+	if len(requires) > 0 {
+		// We use the modfile.SetRequireSeparateIndirect to avoid adding direct
+		// dependencies to the direct block as per:
+		// https://github.com/golang/go/issues/69050
+		modFile.SetRequireSeparateIndirect(append(modFile.Require, requires...))
+	}
+
+	// Add replaces after requires.
+	for _, diff := range replaces {
+		if err := modFile.AddReplace(diff.Name, "", diff.Name, diff.Expected); err != nil {
+			return 0, fmt.Errorf("add replace: %w", err)
 		}
 	}
 
-	return fmt.Errorf("%d incompatibilities found", len(diffs))
+	fixed := len(replaces) + len(requires)
+	if fixed > 0 {
+		modFile.Cleanup()
+		if err := writeModFile(goSum, modFile); err != nil {
+			return 0, err
+		}
+
+		cmd.Printf("%d incompatibilities fixed\n", fixed)
+	}
+
+	return fixed, nil
 }
diff --git a/plugin_test.go b/plugin_test.go
index fea136d..4910a8e 100644
--- a/plugin_test.go
+++ b/plugin_test.go
@@ -2,13 +2,51 @@ package cmd
 
 import (
 	"bytes"
+	"errors"
+	"os"
+	"path/filepath"
+	"strings"
 	"testing"
 
 	"github.com/krakendio/krakend-cobra/v2/plugin"
+	"github.com/luraproject/lura/v2/core"
 	"github.com/spf13/cobra"
 	"github.com/stretchr/testify/require"
 )
 
+const testDir = "testdata"
+
+// copyDir is a helper function to copy directory entries from src to dst.
+func copyDir(t *testing.T, srcSubDir, dstDir string) {
+	t.Helper()
+
+	srcDir := filepath.Join(testDir, srcSubDir)
+	entries, err := os.ReadDir(srcDir)
+	if errors.Is(err, os.ErrNotExist) {
+		// Nothing to do.
+		return
+	}
+	require.NoError(t, err)
+
+	for _, entry := range entries {
+		file := entry.Name()
+		data, err := os.ReadFile(filepath.Join(srcDir, file))
+		require.NoError(t, err)
+
+		err = os.WriteFile(filepath.Join(dstDir, file), data, 0644)
+		require.NoError(t, err)
+	}
+}
+
+// loadFile is a helper function to load a file from the testdata directory.
+func loadFile(t *testing.T, name string) string {
+	t.Helper()
+	data, err := os.ReadFile(filepath.Join(testDir, name))
+	require.NoError(t, err)
+
+	return string(data)
+}
+
 func Test_pluginFuncErr(t *testing.T) {
 	var buf bytes.Buffer
 	cmd := &cobra.Command{}
@@ -16,8 +54,8 @@ func Test_pluginFuncErr(t *testing.T) {
 
 	localDescriber = func() plugin.Descriptor {
 		return plugin.Descriptor{
-			Go:   goVersion,
-			Libc: libcVersion,
+			Go:   core.GoVersion,
+			Libc: core.GlibcVersion,
 			Deps: map[string]string{
 				"golang.org/x/mod":                  "v0.6.0-dev.0.20220419223038-86c51ed26bb4",
 				"github.com/Azure/azure-sdk-for-go": "v59.3.0+incompatible",
@@ -28,63 +66,105 @@ func Test_pluginFuncErr(t *testing.T) {
 
 	defer func() { localDescriber = plugin.Local }()
 
+	goModData := loadFile(t, "go.mod")
+
 	tests := map[string]struct {
-		goSum    string
-		expected string
-		fix      bool
-		err      string
+		dir           string
+		expected      string
+		expectedGoMod string
+		goVersion     string
+		format        bool
+		fix           bool
+		err           string
 	}{
+
 		"missing": {
-			goSum: "./testdata/missing-go.sum",
-			err:   "open ./testdata/missing-go.sum: no such file or directory",
+			dir:           "missing",
+			goVersion:     goVersion,
+			expectedGoMod: goModData,
+			err:           "open DIR/go.sum: no such file or directory",
 		},
-		"matching": {
-			goSum:    "./testdata/match-go.sum",
-			expected: "No incompatibilities found!\n",
+
+		"match": {
+			dir:           "match",
+			goVersion:     goVersion,
+			expectedGoMod: goModData,
+			expected:      "No incompatibilities found!\n",
 		},
 		"changes": {
-			goSum: "./testdata/changes-go.sum",
-			expected: `cloud.google.com/go
-	have: v0.100.3
-	want: v0.100.2
-github.com/Azure/azure-sdk-for-go
-	have: v59.3.1+incompatible
-	want: v59.3.0+incompatible
-golang.org/x/mod
-	have: v0.6.10-dev.0.20220419223038-86c51ed26bb4
-	want: v0.6.0-dev.0.20220419223038-86c51ed26bb4
-`,
-			err: "3 incompatibilities found",
+			dir:           "changes",
+			goVersion:     goVersion,
+			expectedGoMod: goModData,
+			expected:      loadFile(t, "changes/expected.txt"),
+			err:           "3 incompatibilities found",
 		},
-		"fix": {
-			goSum: "./testdata/changes-go.sum",
-			fix:   true,
-			expected: `go mod edit --replace cloud.google.com/go=cloud.google.com/go@v0.100.2
-go mod edit --replace github.com/Azure/azure-sdk-for-go=github.com/Azure/azure-sdk-for-go@v59.3.0+incompatible
-go get golang.org/x/mod@v0.6.0-dev.0.20220419223038-86c51ed26bb4
+		"format": {
+			dir:           "changes",
+			goVersion:     goVersion,
+			expectedGoMod: goModData,
+			format:        true,
+			expected:      loadFile(t, "format/expected.txt"),
+			err:           "3 incompatibilities found",
+		},
+		"fixed-all": {
+			dir:           "changes",
+			goVersion:     goVersion,
+			expectedGoMod: loadFile(t, "fixed-all/go.mod"),
+			fix:           true,
+			expected:      "3 incompatibilities fixed\n",
+		},
+		"fixed-some": {
+			dir:           "changes",
+			goVersion:     "1.1.0",
+			expectedGoMod: loadFile(t, "fixed-some/go.mod"),
+			fix:           true,
+			expected: `go
+	have: 1.1.0
+	want: undefined
+3 incompatibilities fixed
 `,
-			err: "3 incompatibilities found",
+			err: "3 incompatibilities fixed, 1 left",
 		},
 	}
 	for name, tc := range tests {
 		t.Run(name, func(t *testing.T) {
 			buf.Reset()
 
+			// Make copies in a temporary directory so
+			// the original files are not modified.
+			tempDir := t.TempDir()
 			orig := goSum
-			goSum = tc.goSum
+			goSum = filepath.Join(tempDir, "go.sum")
+			copyDir(t, tc.dir, tempDir)
 			defer func() { goSum = orig }()
 
-			fix := gogetEnabled
-			gogetEnabled = tc.fix
-			defer func() { gogetEnabled = fix }()
+			// Override the global variables for the test.
+			format := gogetEnabled
+			fix := fixEnabled
+			gogetEnabled = tc.format
+			fixEnabled = tc.fix
+			oldGoVersion := goVersion
+			goVersion = tc.goVersion
+			defer func() {
+				gogetEnabled = format
+				fixEnabled = fix
+				goVersion = oldGoVersion
+			}()
 
 			err := pluginFuncErr(cmd, nil)
 			if tc.err != "" {
-				require.EqualError(t, err, tc.err)
+				require.EqualError(t, err, strings.ReplaceAll(tc.err, "DIR", tempDir))
 			} else {
 				require.NoError(t, err)
 			}
 			require.Equal(t, tc.expected, buf.String())
+
+			data, err := os.ReadFile(filepath.Join(tempDir, "go.mod"))
+			if errors.Is(err, os.ErrNotExist) {
+				return
+			}
+			require.NoError(t, err)
+			require.Equal(t, string(tc.expectedGoMod), string(data))
 		})
 	}
 }
diff --git a/root.go b/root.go
index 914efba..0967dfd 100644
--- a/root.go
+++ b/root.go
@@ -31,6 +31,7 @@ var (
 	libcVersion     = core.GlibcVersion
 	checkDumpPrefix = "\t"
 	gogetEnabled    = false
+	fixEnabled      = false
 
 	DefaultRoot    Root
 	RootCommand    Command
@@ -110,13 +111,14 @@ func init() {
 	goVersionFlag := StringFlagBuilder(&goVersion, "go", "g", goVersion, "The version of the go compiler used for your plugin")
 	libcVersionFlag := StringFlagBuilder(&libcVersion, "libc", "l", "", "Version of the libc library used")
 	gogetFlag := BoolFlagBuilder(&gogetEnabled, "format", "f", false, "Shows fix commands to update your dependencies")
+	fixFlag := BoolFlagBuilder(&fixEnabled, "fix", "x", false, "Applies fixes to update your dependencies")
 	PluginCommand = NewCommand(pluginCmd, goSumFlag, goVersionFlag, libcVersionFlag, gogetFlag)
 
 	rulesToExcludeFlag := StringFlagBuilder(&rulesToExclude, "ignore", "i", rulesToExclude, "List of rules to ignore (comma-separated, no spaces)")
 	severitiesToIncludeFlag := StringFlagBuilder(&severitiesToInclude, "severity", "s", severitiesToInclude, "List of severities to include (comma-separated, no spaces)")
 	pathToRulesToExcludeFlag := StringFlagBuilder(&rulesToExcludePath, "ignore-file", "I", rulesToExcludePath, "Path to a text-plain file containing the list of rules to exclude")
 	formatFlag := StringFlagBuilder(&formatTmpl, "format", "f", formatTmpl, "Inline go template to render the results")
-	AuditCommand = NewCommand(auditCmd, cfgFlag, rulesToExcludeFlag, severitiesToIncludeFlag, pathToRulesToExcludeFlag, formatFlag)
+	AuditCommand = NewCommand(auditCmd, cfgFlag, rulesToExcludeFlag, severitiesToIncludeFlag, pathToRulesToExcludeFlag, formatFlag, fixFlag)
 
 	VersionCommand = NewCommand(versionCmd)
 
diff --git a/testdata/changes/expected.txt b/testdata/changes/expected.txt
new file mode 100644
index 0000000..4ed20d7
--- /dev/null
+++ b/testdata/changes/expected.txt
@@ -0,0 +1,9 @@
+cloud.google.com/go
+	have: v0.100.3
+	want: v0.100.2
+github.com/Azure/azure-sdk-for-go
+	have: v59.3.1+incompatible
+	want: v59.3.0+incompatible
+golang.org/x/mod
+	have: v0.6.10-dev.0.20220419223038-86c51ed26bb4
+	want: v0.6.0-dev.0.20220419223038-86c51ed26bb4
diff --git a/testdata/changes/go.mod b/testdata/changes/go.mod
new file mode 100644
index 0000000..c429cbf
--- /dev/null
+++ b/testdata/changes/go.mod
@@ -0,0 +1,13 @@
+module github.com/krakendio/krakend-cobra/v2
+
+go 1.17
+
+require (
+	github.com/gin-gonic/gin v1.8.2
+	golang.org/x/mod v0.6.0-dev.0.20220419223038-86c51ed26bb4
+)
+
+require (
+	cloud.google.com/go v0.100.2 // indirect
+	github.com/Azure/azure-sdk-for-go v59.3.0+incompatible // indirect
+)
diff --git a/testdata/changes-go.sum b/testdata/changes/go.sum
similarity index 100%
rename from testdata/changes-go.sum
rename to testdata/changes/go.sum
diff --git a/testdata/fixed-all/go.mod b/testdata/fixed-all/go.mod
new file mode 100644
index 0000000..73a409d
--- /dev/null
+++ b/testdata/fixed-all/go.mod
@@ -0,0 +1,17 @@
+module github.com/krakendio/krakend-cobra/v2
+
+go 1.17
+
+require (
+	github.com/gin-gonic/gin v1.8.2
+	golang.org/x/mod v0.6.0-dev.0.20220419223038-86c51ed26bb4
+)
+
+require (
+	cloud.google.com/go v0.100.2 // indirect
+	github.com/Azure/azure-sdk-for-go v59.3.0+incompatible // indirect
+)
+
+replace cloud.google.com/go => cloud.google.com/go v0.100.2
+
+replace github.com/Azure/azure-sdk-for-go => github.com/Azure/azure-sdk-for-go v59.3.0+incompatible
diff --git a/testdata/fixed-some/go.mod b/testdata/fixed-some/go.mod
new file mode 100644
index 0000000..73a409d
--- /dev/null
+++ b/testdata/fixed-some/go.mod
@@ -0,0 +1,17 @@
+module github.com/krakendio/krakend-cobra/v2
+
+go 1.17
+
+require (
+	github.com/gin-gonic/gin v1.8.2
+	golang.org/x/mod v0.6.0-dev.0.20220419223038-86c51ed26bb4
+)
+
+require (
+	cloud.google.com/go v0.100.2 // indirect
+	github.com/Azure/azure-sdk-for-go v59.3.0+incompatible // indirect
+)
+
+replace cloud.google.com/go => cloud.google.com/go v0.100.2
+
+replace github.com/Azure/azure-sdk-for-go => github.com/Azure/azure-sdk-for-go v59.3.0+incompatible
diff --git a/testdata/format/expected.txt b/testdata/format/expected.txt
new file mode 100644
index 0000000..79efa61
--- /dev/null
+++ b/testdata/format/expected.txt
@@ -0,0 +1,3 @@
+go mod edit --replace cloud.google.com/go=cloud.google.com/go@v0.100.2
+go mod edit --replace github.com/Azure/azure-sdk-for-go=github.com/Azure/azure-sdk-for-go@v59.3.0+incompatible
+go get golang.org/x/mod@v0.6.0-dev.0.20220419223038-86c51ed26bb4
diff --git a/testdata/match/go.mod b/testdata/match/go.mod
new file mode 100644
index 0000000..c429cbf
--- /dev/null
+++ b/testdata/match/go.mod
@@ -0,0 +1,13 @@
+module github.com/krakendio/krakend-cobra/v2
+
+go 1.17
+
+require (
+	github.com/gin-gonic/gin v1.8.2
+	golang.org/x/mod v0.6.0-dev.0.20220419223038-86c51ed26bb4
+)
+
+require (
+	cloud.google.com/go v0.100.2 // indirect
+	github.com/Azure/azure-sdk-for-go v59.3.0+incompatible // indirect
+)
diff --git a/testdata/match-go.sum b/testdata/match/go.sum
similarity index 100%
rename from testdata/match-go.sum
rename to testdata/match/go.sum