diff --git a/cmd/root.go b/cmd/root.go
index b5f342cc..377b1fbe 100644
--- a/cmd/root.go
+++ b/cmd/root.go
@@ -72,7 +72,7 @@ var RootCmd = &cobra.Command{
 				logrus.Error(err)
 			}
 			if !cfg.IsDryRun() {
-				if err := cfg.SaveConfig(); err != nil {
+				if err := cfg.UpdateConfig(); err != nil {
 					// TODO(log): Better error message
 					logrus.Error(err)
 				}
diff --git a/go.mod b/go.mod
index 732c5a2a..e53a56b1 100644
--- a/go.mod
+++ b/go.mod
@@ -16,6 +16,8 @@ require (
 	github.com/fsnotify/fsnotify v1.6.0
 	github.com/google/go-github/v53 v53.2.0
 	github.com/magefile/mage v1.15.0
+	github.com/mitchellh/mapstructure v1.5.0
+	github.com/pelletier/go-toml/v2 v2.0.8
 	github.com/sirupsen/logrus v1.9.3
 	github.com/spf13/cobra v1.7.0
 	github.com/spf13/viper v1.16.0
@@ -25,6 +27,7 @@ require (
 	github.com/uwu-tools/magex v0.10.0
 	golang.org/x/oauth2 v0.11.0
 	golang.org/x/term v0.11.0
+	gopkg.in/yaml.v3 v3.0.1
 	sigs.k8s.io/release-sdk v0.10.3
 	sigs.k8s.io/release-utils v0.7.5-0.20230814131120-e16435f5a2de
 )
@@ -59,9 +62,7 @@ require (
 	github.com/klauspost/pgzip v1.2.5 // indirect
 	github.com/magiconair/properties v1.8.7 // indirect
 	github.com/mholt/archiver/v3 v3.5.1 // indirect
-	github.com/mitchellh/mapstructure v1.5.0 // indirect
 	github.com/nwaples/rardecode v1.1.0 // indirect
-	github.com/pelletier/go-toml/v2 v2.0.8 // indirect
 	github.com/pierrec/lz4/v4 v4.1.2 // indirect
 	github.com/pjbgf/sha1cd v0.3.0 // indirect
 	github.com/pmezard/go-difflib v1.0.0 // indirect
@@ -85,6 +86,5 @@ require (
 	google.golang.org/protobuf v1.31.0 // indirect
 	gopkg.in/ini.v1 v1.67.0 // indirect
 	gopkg.in/warnings.v0 v0.1.2 // indirect
-	gopkg.in/yaml.v3 v3.0.1 // indirect
 	k8s.io/utils v0.0.0-20230406110748-d93618cff8a2 // indirect
 )
diff --git a/internal/config/config.go b/internal/config/config.go
index eb8ba982..0c1e63c2 100644
--- a/internal/config/config.go
+++ b/internal/config/config.go
@@ -18,7 +18,6 @@ package config
 
 import (
 	"context"
-	"encoding/json"
 	"errors"
 	"fmt"
 	"io"
@@ -31,12 +30,17 @@ import (
 
 	"github.com/dghubble/oauth1"
 	"github.com/fsnotify/fsnotify"
+	"github.com/mitchellh/mapstructure"
 	log "github.com/sirupsen/logrus"
 	"github.com/spf13/cobra"
 	"github.com/spf13/viper"
 	jira "github.com/uwu-tools/go-jira/v2/cloud"
 	"golang.org/x/term"
 
+	"github.com/uwu-tools/gh-jira-issue-sync/internal/encoding"
+	"github.com/uwu-tools/gh-jira-issue-sync/internal/encoding/json"
+	"github.com/uwu-tools/gh-jira-issue-sync/internal/encoding/toml"
+	"github.com/uwu-tools/gh-jira-issue-sync/internal/encoding/yaml"
 	"github.com/uwu-tools/gh-jira-issue-sync/internal/github"
 	"github.com/uwu-tools/gh-jira-issue-sync/internal/options"
 )
@@ -78,6 +82,9 @@ type Config struct {
 	// cmdFile is the file Viper is using for its configuration.
 	cmdFile string
 
+	// cmdFileType is the extension of the config file
+	cmdFileType string
+
 	// cmdConfig is the Viper configuration object created from the command line and config file.
 	cmdConfig viper.Viper
 
@@ -94,6 +101,9 @@ type Config struct {
 	// project represents the Jira project the user has requested.
 	project *jira.Project
 
+	// encoderRegistry is used for encoding the config file to supported Viper types
+	encoderRegistry *encoding.EncoderRegistry
+
 	// since is the parsed value of the `since` configuration parameter, which is the earliest that
 	// a GitHub issue can have been updated to be retrieved.
 	since time.Time
@@ -132,7 +142,8 @@ func New(ctx context.Context, cmd *cobra.Command) (*Config, error) {
 
 	log.Debugf("using config file: %s", cfgFilePath)
 	cfg.cmdFile = cfgFilePath
-	cfg.cmdConfig = *newViper(options.AppName, cfg.cmdFile)
+	cfg.cmdFileType = getConfigTypeFromName(cfgFilePath)
+	cfg.cmdConfig = *newViper(options.AppName, cfg.cmdFile, cfg.cmdFileType)
 	cfg.cmdConfig.BindPFlags(cmd.Flags()) //nolint:errcheck
 
 	cfg.cmdFile = cfg.cmdConfig.ConfigFileUsed()
@@ -143,6 +154,10 @@ func New(ctx context.Context, cmd *cobra.Command) (*Config, error) {
 		return nil, err
 	}
 
+	if err := cfg.resetEncoding(); err != nil {
+		return nil, err
+	}
+
 	return &cfg, nil
 }
 
@@ -272,24 +287,24 @@ func (c *Config) SetJiraToken(token *oauth1.Token) {
 
 // configFile is a serializable representation of the current Viper configuration.
 type configFile struct {
-	LogLevel    string        `json:"log-level,omitempty" mapstructure:"log-level"`
-	GithubToken string        `json:"github-token,omitempty" mapstructure:"github-token"`
-	JiraUser    string        `json:"jira-user,omitempty" mapstructure:"jira-user"`
-	JiraPass    string        `json:"jira-pass,omitempty" mapstructure:"jira-pass"`
-	JiraToken   string        `json:"jira-token,omitempty" mapstructure:"jira-token"`
-	JiraSecret  string        `json:"jira-secret,omitempty" mapstructure:"jira-secret"`
-	JiraKey     string        `json:"jira-private-key-path,omitempty" mapstructure:"jira-private-key-path"`
-	JiraCKey    string        `json:"jira-consumer-key,omitempty" mapstructure:"jira-consumer-key"`
-	RepoName    string        `json:"repo-name,omitempty" mapstructure:"repo-name"`
-	JiraURI     string        `json:"jira-uri,omitempty" mapstructure:"jira-uri"`
-	JiraProject string        `json:"jira-project,omitempty" mapstructure:"jira-project"`
-	Since       string        `json:"since,omitempty" mapstructure:"since"`
-	Confirm     bool          `json:"confirm,omitempty" mapstructure:"confirm"`
-	Timeout     time.Duration `json:"timeout,omitempty" mapstructure:"timeout"`
+	LogLevel    string        `mapstructure:"log-level,omitempty"`
+	GithubToken string        `mapstructure:"github-token,omitempty"`
+	JiraUser    string        `mapstructure:"jira-user,omitempty"`
+	JiraPass    string        `mapstructure:"jira-pass,omitempty"`
+	JiraToken   string        `mapstructure:"jira-token,omitempty"`
+	JiraSecret  string        `mapstructure:"jira-secret,omitempty"`
+	JiraKey     string        `mapstructure:"jira-private-key-path,omitempty"`
+	JiraCKey    string        `mapstructure:"jira-consumer-key,omitempty"`
+	RepoName    string        `mapstructure:"repo-name,omitempty"`
+	JiraURI     string        `mapstructure:"jira-uri,omitempty"`
+	JiraProject string        `mapstructure:"jira-project,omitempty"`
+	Since       string        `mapstructure:"since,omitempty"`
+	Confirm     bool          `mapstructure:"confirm,omitempty"`
+	Timeout     time.Duration `mapstructure:"timeout,omitempty"`
 }
 
-// SaveConfig updates the `since` parameter to now, then saves the configuration file.
-func (c *Config) SaveConfig() error {
+// UpdateConfig updates the `since` parameter to now, then saves the configuration file.
+func (c *Config) UpdateConfig() error {
 	c.cmdConfig.Set(
 		options.ConfigKeySince,
 		time.Now().Format(options.DateFormat),
@@ -300,9 +315,14 @@ func (c *Config) SaveConfig() error {
 		return fmt.Errorf("unmarshalling config: %w", err)
 	}
 
-	b, err := json.MarshalIndent(cf, "", "  ")
+	cfMap := make(map[string]interface{})
+	if err := mapstructure.Decode(cf, &cfMap); err != nil {
+		return fmt.Errorf("decoding configFile struct to map[string]interface{}: %w", err)
+	}
+
+	b, err := c.encoderRegistry.Encode(c.cmdFileType, cfMap)
 	if err != nil {
-		return fmt.Errorf("marshalling config: %w", err)
+		return fmt.Errorf("encoding config to %s format: %w", c.cmdFileType, err)
 	}
 
 	f, err := os.OpenFile(c.cmdConfig.ConfigFileUsed(), os.O_RDWR|os.O_TRUNC|os.O_CREATE, 0o644)
@@ -324,7 +344,7 @@ func (c *Config) SaveConfig() error {
 // command line options, configuration file options, and
 // default configuration values. This viper object becomes
 // the single source of truth for the app configuration.
-func newViper(appName, cfgFile string) *viper.Viper {
+func newViper(appName, cfgFile, cfgFileType string) *viper.Viper {
 	logger := log.New()
 	v := viper.New()
 
@@ -337,7 +357,7 @@ func newViper(appName, cfgFile string) *viper.Viper {
 	if cfgFile != "" {
 		v.SetConfigFile(cfgFile)
 	}
-	v.SetConfigType(getConfigTypeFromName(cfgFile))
+	v.SetConfigType(cfgFileType)
 
 	if err := v.ReadInConfig(); err == nil {
 		log.WithField("file", v.ConfigFileUsed()).Infof("config file loaded")
@@ -517,6 +537,45 @@ func (c *Config) getFieldIDs(client *jira.Client) (*fields, error) {
 	return &fieldIDs, nil
 }
 
+// resetEncoding creates a new encoding registry with the currently supported file formats.
+func (c *Config) resetEncoding() error {
+	encoderRegistry := encoding.NewEncoderRegistry()
+	registerEncoder := func(format string, codec encoding.Encoder) error {
+		if err := encoderRegistry.RegisterEncoder(format, codec); err != nil {
+			return fmt.Errorf("registering encoder for %s extension: %w", format, err)
+		}
+
+		return nil
+	}
+
+	{
+		codec := &yaml.Codec{}
+		if err := registerEncoder("yaml", codec); err != nil {
+			return err
+		}
+		if err := registerEncoder("yml", codec); err != nil {
+			return err
+		}
+	}
+
+	{
+		codec := &json.Codec{}
+		if err := registerEncoder("json", codec); err != nil {
+			return err
+		}
+	}
+
+	{
+		codec := &toml.Codec{}
+		if err := registerEncoder("toml", codec); err != nil {
+			return err
+		}
+	}
+
+	c.encoderRegistry = encoderRegistry
+	return nil
+}
+
 // Errors
 
 var (
@@ -543,12 +602,12 @@ func errCustomFieldIDNotFound(field string) error {
 // getConfigTypeFromName extracts the extension from the passed in filename,
 // returns `json` if it's empty.
 func getConfigTypeFromName(filename string) string {
-	if filename == "" {
+	// it's enough to rely on the type from the filename because
+	// viper will parse and validate the the file's content
+	ext := filepath.Ext(filename)
+	if ext == "" {
 		return "json"
 	}
 
-	// it's enough to rely on the type from the filename because
-	// viper will parse and validate the the file's content
-	parts := strings.Split(filename, ".")
-	return parts[len(parts)-1]
+	return strings.TrimPrefix(ext, ".")
 }
diff --git a/internal/encoding/encoder.go b/internal/encoding/encoder.go
new file mode 100644
index 00000000..a4ba86d0
--- /dev/null
+++ b/internal/encoding/encoder.go
@@ -0,0 +1,66 @@
+package encoding
+
+import (
+	"fmt"
+	"sync"
+)
+
+// Encoder encodes the contents of v into a byte representation.
+// It's primarily used for encoding a map[string]interface{} into a file format.
+type Encoder interface {
+	Encode(v map[string]interface{}) ([]byte, error)
+}
+
+const (
+	// ErrEncoderNotFound is returned when there is no encoder registered for a format.
+	ErrEncoderNotFound = encodingError("encoder not found for this format")
+
+	// ErrEncoderFormatAlreadyRegistered is returned when an encoder is already registered for a format.
+	ErrEncoderFormatAlreadyRegistered = encodingError("encoder already registered for this format")
+)
+
+// EncoderRegistry can choose an appropriate Encoder based on the provided format.
+type EncoderRegistry struct {
+	encoders map[string]Encoder
+
+	mu sync.RWMutex
+}
+
+// NewEncoderRegistry returns a new, initialized EncoderRegistry.
+func NewEncoderRegistry() *EncoderRegistry {
+	return &EncoderRegistry{
+		encoders: make(map[string]Encoder),
+	}
+}
+
+// RegisterEncoder registers an Encoder for a format.
+// Registering a Encoder for an already existing format is not supported.
+func (e *EncoderRegistry) RegisterEncoder(format string, enc Encoder) error {
+	e.mu.Lock()
+	defer e.mu.Unlock()
+
+	if _, ok := e.encoders[format]; ok {
+		return ErrEncoderFormatAlreadyRegistered
+	}
+
+	e.encoders[format] = enc
+
+	return nil
+}
+
+func (e *EncoderRegistry) Encode(format string, v map[string]interface{}) ([]byte, error) {
+	e.mu.RLock()
+	encoder, ok := e.encoders[format]
+	e.mu.RUnlock()
+
+	if !ok {
+		return nil, ErrEncoderNotFound
+	}
+
+	b, err := encoder.Encode(v)
+	if err != nil {
+		return nil, fmt.Errorf("encoding map to %s format: %w", format, err)
+	}
+
+	return b, nil
+}
diff --git a/internal/encoding/error.go b/internal/encoding/error.go
new file mode 100644
index 00000000..e4cde02d
--- /dev/null
+++ b/internal/encoding/error.go
@@ -0,0 +1,7 @@
+package encoding
+
+type encodingError string
+
+func (e encodingError) Error() string {
+	return string(e)
+}
diff --git a/internal/encoding/json/codec.go b/internal/encoding/json/codec.go
new file mode 100644
index 00000000..84dec1c2
--- /dev/null
+++ b/internal/encoding/json/codec.go
@@ -0,0 +1,24 @@
+package json
+
+import (
+	"encoding/json"
+	"fmt"
+)
+
+// Codec implements the encoding.Encoder interface for JSON encoding.
+type Codec struct {
+	// prefix for JSON marshal.
+	Prefix string
+
+	// indentation for JSON marshal.
+	Indent string
+}
+
+func (c *Codec) Encode(v map[string]interface{}) ([]byte, error) {
+	b, err := json.MarshalIndent(v, c.Prefix, c.Indent)
+	if err != nil {
+		return nil, fmt.Errorf("json marshalling value: %w", err)
+	}
+
+	return b, nil
+}
diff --git a/internal/encoding/json/codec_test.go b/internal/encoding/json/codec_test.go
new file mode 100644
index 00000000..27ec79d1
--- /dev/null
+++ b/internal/encoding/json/codec_test.go
@@ -0,0 +1,59 @@
+package json
+
+import (
+	"testing"
+
+	"github.com/stretchr/testify/require"
+)
+
+const encoded = `{
+  "key": "value",
+  "list": [
+    "item1",
+    "item2",
+    "item3"
+  ],
+  "map": {
+    "key": "value"
+  },
+  "nested_map": {
+    "map": {
+      "key": "value",
+      "list": [
+        "item1",
+        "item2",
+        "item3"
+      ]
+    }
+  }
+}`
+
+var data = map[string]interface{}{
+	"key": "value",
+	"list": []interface{}{
+		"item1",
+		"item2",
+		"item3",
+	},
+	"map": map[string]interface{}{
+		"key": "value",
+	},
+	"nested_map": map[string]interface{}{
+		"map": map[string]interface{}{
+			"key": "value",
+			"list": []interface{}{
+				"item1",
+				"item2",
+				"item3",
+			},
+		},
+	},
+}
+
+func TestCodec_Encode(t *testing.T) {
+	codec := Codec{}
+
+	b, err := codec.Encode(data)
+	require.Empty(t, err)
+	require.Equal(t, encoded, string(b))
+}
diff --git a/internal/encoding/toml/codec.go b/internal/encoding/toml/codec.go
new file mode 100644
index 00000000..140445b6
--- /dev/null
+++ b/internal/encoding/toml/codec.go
@@ -0,0 +1,19 @@
+package toml
+
+import (
+	"fmt"
+
+	"github.com/pelletier/go-toml/v2"
+)
+
+// Codec implements the encoding.Encoder interface for TOML encoding.
+type Codec struct{}
+
+func (Codec) Encode(v map[string]interface{}) ([]byte, error) {
+	b, err := toml.Marshal(v)
+	if err != nil {
+		return nil, fmt.Errorf("toml marshalling value: %w", err)
+	}
+
+	return b, nil
+}
diff --git a/internal/encoding/toml/codec_test.go b/internal/encoding/toml/codec_test.go
new file mode 100644
index 00000000..dc503858
--- /dev/null
+++ b/internal/encoding/toml/codec_test.go
@@ -0,0 +1,49 @@
+package toml
+
+import (
+	"testing"
+
+	"github.com/stretchr/testify/require"
+)
+
+const encoded = `key = 'value'
+list = ['item1', 'item2', 'item3']
+
+[map]
+key = 'value'
+
+[nested_map]
+[nested_map.map]
+key = 'value'
+list = ['item1', 'item2', 'item3']
+`
+
+var data = map[string]interface{}{
+	"key": "value",
+	"list": []interface{}{
+		"item1",
+		"item2",
+		"item3",
+	},
+	"map": map[string]interface{}{
+		"key": "value",
+	},
+	"nested_map": map[string]interface{}{
+		"map": map[string]interface{}{
+			"key": "value",
+			"list": []interface{}{
+				"item1",
+				"item2",
+				"item3",
+			},
+		},
+	},
+}
+
+func TestCodec_Encode(t *testing.T) {
+	codec := Codec{}
+
+	b, err := codec.Encode(data)
+	require.Empty(t, err)
+	require.Equal(t, encoded, string(b))
+}
diff --git a/internal/encoding/yaml/codec.go b/internal/encoding/yaml/codec.go
new file mode 100644
index 00000000..fa5391f5
--- /dev/null
+++ b/internal/encoding/yaml/codec.go
@@ -0,0 +1,19 @@
+package yaml
+
+import (
+	"fmt"
+
+	"gopkg.in/yaml.v3"
+)
+
+// Codec implements the encoding.Encoder interfaces for YAML encoding.
+type Codec struct{}
+
+func (Codec) Encode(v map[string]interface{}) ([]byte, error) {
+	b, err := yaml.Marshal(v)
+	if err != nil {
+		return nil, fmt.Errorf("yaml marshalling value: %w", err)
+	}
+
+	return b, nil
+}
diff --git a/internal/encoding/yaml/codec_test.go b/internal/encoding/yaml/codec_test.go
new file mode 100644
index 00000000..ed21fac5
--- /dev/null
+++ b/internal/encoding/yaml/codec_test.go
@@ -0,0 +1,53 @@
+package yaml
+
+import (
+	"testing"
+
+	"github.com/stretchr/testify/require"
+)
+
+const encoded = `key: value
+list:
+    - item1
+    - item2
+    - item3
+map:
+    key: value
+nested_map:
+    map:
+        key: value
+        list:
+            - item1
+            - item2
+            - item3
+`
+
+var data = map[string]interface{}{
+	"key": "value",
+	"list": []interface{}{
+		"item1",
+		"item2",
+		"item3",
+	},
+	"map": map[string]interface{}{
+		"key": "value",
+	},
+	"nested_map": map[string]interface{}{
+		"map": map[string]interface{}{
+			"key": "value",
+			"list": []interface{}{
+				"item1",
+				"item2",
+				"item3",
+			},
+		},
+	},
+}
+
+func TestCodec_Encode(t *testing.T) {
+	codec := Codec{}
+
+	b, err := codec.Encode(data)
+	require.Empty(t, err)
+	require.Equal(t, encoded, string(b))
+}