diff --git a/pkg/config/user_config.go b/pkg/config/user_config.go
index 116f63487..a1bbe09a6 100644
--- a/pkg/config/user_config.go
+++ b/pkg/config/user_config.go
@@ -619,7 +619,8 @@ type CustomCommand struct {
 	// The command to run (using Go template syntax for placeholder values)
 	Command string `yaml:"command" jsonschema:"example=git fetch {{.Form.Remote}} {{.Form.Branch}} && git checkout FETCH_HEAD"`
 	// If true, run the command in a subprocess (e.g. if the command requires user input)
-	Subprocess bool `yaml:"subprocess"`
+	// [dev] Pointer to bool so that we can distinguish unset (nil) from false.
+	Subprocess *bool `yaml:"subprocess"`
 	// A list of prompts that will request user input before running the final command
 	Prompts []CustomCommandPrompt `yaml:"prompts"`
 	// Text to display while waiting for command to finish
@@ -627,13 +628,16 @@ type CustomCommand struct {
 	// Label for the custom command when displayed in the keybindings menu
 	Description string `yaml:"description"`
 	// If true, stream the command's output to the Command Log panel
-	Stream bool `yaml:"stream"`
+	// [dev] Pointer to bool so that we can distinguish unset (nil) from false.
+	Stream *bool `yaml:"stream"`
 	// If true, show the command's output in a popup within Lazygit
-	ShowOutput bool `yaml:"showOutput"`
+	// [dev] Pointer to bool so that we can distinguish unset (nil) from false.
+	ShowOutput *bool `yaml:"showOutput"`
 	// The title to display in the popup panel if showOutput is true. If left unset, the command will be used as the title.
 	OutputTitle string `yaml:"outputTitle"`
 	// Actions to take after the command has completed
-	After CustomCommandAfterHook `yaml:"after"`
+	// [dev] Pointer so that we can tell whether it appears in the config file
+	After *CustomCommandAfterHook `yaml:"after"`
 }
 
 type CustomCommandPrompt struct {
diff --git a/pkg/gui/services/custom_commands/handler_creator.go b/pkg/gui/services/custom_commands/handler_creator.go
index 95de40a2e..9e17ca9fa 100644
--- a/pkg/gui/services/custom_commands/handler_creator.go
+++ b/pkg/gui/services/custom_commands/handler_creator.go
@@ -261,7 +261,7 @@ func (self *HandlerCreator) finalHandler(customCommand config.CustomCommand, ses
 
 	cmdObj := self.c.OS().Cmd.NewShell(cmdStr)
 
-	if customCommand.Subprocess {
+	if customCommand.Subprocess != nil && *customCommand.Subprocess {
 		return self.c.RunSubprocessAndRefresh(cmdObj)
 	}
 
@@ -273,7 +273,7 @@ func (self *HandlerCreator) finalHandler(customCommand config.CustomCommand, ses
 	return self.c.WithWaitingStatus(loadingText, func(gocui.Task) error {
 		self.c.LogAction(self.c.Tr.Actions.CustomCommand)
 
-		if customCommand.Stream {
+		if customCommand.Stream != nil && *customCommand.Stream {
 			cmdObj.StreamOutput()
 		}
 		output, err := cmdObj.RunWithOutput()
@@ -283,14 +283,14 @@ func (self *HandlerCreator) finalHandler(customCommand config.CustomCommand, ses
 		}
 
 		if err != nil {
-			if customCommand.After.CheckForConflicts {
+			if customCommand.After != nil && customCommand.After.CheckForConflicts {
 				return self.mergeAndRebaseHelper.CheckForConflicts(err)
 			}
 
 			return err
 		}
 
-		if customCommand.ShowOutput {
+		if customCommand.ShowOutput != nil && *customCommand.ShowOutput {
 			if strings.TrimSpace(output) == "" {
 				output = self.c.Tr.EmptyOutput
 			}
diff --git a/pkg/integration/tests/custom_commands/check_for_conflicts.go b/pkg/integration/tests/custom_commands/check_for_conflicts.go
index 024f32733..25f1d2097 100644
--- a/pkg/integration/tests/custom_commands/check_for_conflicts.go
+++ b/pkg/integration/tests/custom_commands/check_for_conflicts.go
@@ -19,7 +19,7 @@ var CheckForConflicts = NewIntegrationTest(NewIntegrationTestArgs{
 				Key:     "m",
 				Context: "localBranches",
 				Command: "git merge {{ .SelectedLocalBranch.Name | quote }}",
-				After: config.CustomCommandAfterHook{
+				After: &config.CustomCommandAfterHook{
 					CheckForConflicts: true,
 				},
 			},
diff --git a/pkg/integration/tests/custom_commands/show_output_in_panel.go b/pkg/integration/tests/custom_commands/show_output_in_panel.go
index 171a477d8..7f00d8a5b 100644
--- a/pkg/integration/tests/custom_commands/show_output_in_panel.go
+++ b/pkg/integration/tests/custom_commands/show_output_in_panel.go
@@ -15,18 +15,19 @@ var ShowOutputInPanel = NewIntegrationTest(NewIntegrationTestArgs{
 		shell.EmptyCommit("my change")
 	},
 	SetupConfig: func(cfg *config.AppConfig) {
+		trueVal := true
 		cfg.GetUserConfig().CustomCommands = []config.CustomCommand{
 			{
 				Key:        "X",
 				Context:    "commits",
 				Command:    "printf '%s' '{{ .SelectedLocalCommit.Name }}'",
-				ShowOutput: true,
+				ShowOutput: &trueVal,
 			},
 			{
 				Key:         "Y",
 				Context:     "commits",
 				Command:     "printf '%s' '{{ .SelectedLocalCommit.Name }}'",
-				ShowOutput:  true,
+				ShowOutput:  &trueVal,
 				OutputTitle: "Subject of commit {{ .SelectedLocalCommit.Hash }}",
 			},
 		}