diff --git a/pkg/commands/git_commands/submodule.go b/pkg/commands/git_commands/submodule.go
index 3eb081701..d8c1208bc 100644
--- a/pkg/commands/git_commands/submodule.go
+++ b/pkg/commands/git_commands/submodule.go
@@ -28,10 +28,15 @@ func NewSubmoduleCommands(gitCommon *GitCommon) *SubmoduleCommands {
 }
 
 func (self *SubmoduleCommands) GetConfigs(parentModule *models.SubmoduleConfig) ([]*models.SubmoduleConfig, error) {
-	gitModulesPath := ".gitmodules"
+	// Resolve the path against the repo this commands object was created for
+	// rather than the process working directory, so that a read from a
+	// still-running refresh keeps addressing that repo after the user
+	// switched to another one.
+	dir := self.repoPaths.WorktreePath()
 	if parentModule != nil {
-		gitModulesPath = filepath.Join(parentModule.FullPath(), gitModulesPath)
+		dir = filepath.Join(dir, parentModule.FullPath())
 	}
+	gitModulesPath := filepath.Join(dir, ".gitmodules")
 	file, err := os.Open(gitModulesPath)
 	if err != nil {
 		if os.IsNotExist(err) {
@@ -180,7 +185,7 @@ func (self *SubmoduleCommands) ConflictSideLog(path string, side string, otherSi
 func (self *SubmoduleCommands) Stash(submodule *models.SubmoduleConfig) error {
 	// if the path does not exist then it hasn't yet been initialized so we'll swallow the error
 	// because the intention here is to have no dirty worktree state
-	if _, err := os.Stat(submodule.Path); os.IsNotExist(err) {
+	if _, err := os.Stat(filepath.Join(self.repoPaths.WorktreePath(), submodule.FullPath())); os.IsNotExist(err) {
 		self.Log.Infof("submodule path %s does not exist, returning", submodule.FullPath())
 		return nil
 	}
diff --git a/pkg/gui/controllers/helpers/refresh_helper.go b/pkg/gui/controllers/helpers/refresh_helper.go
index 27f465f69..8ae62d9dd 100644
--- a/pkg/gui/controllers/helpers/refresh_helper.go
+++ b/pkg/gui/controllers/helpers/refresh_helper.go
@@ -1,6 +1,7 @@
 package helpers
 
 import (
+	"path/filepath"
 	"strings"
 	"sync"
 	"sync/atomic"
@@ -1273,7 +1274,11 @@ func (self *RefreshHelper) refreshStateFiles(captured capturedFilesState, env re
 				prevConflictFileCount++
 			}
 			if file.HasInlineMergeConflicts {
-				hasConflicts, err := mergeconflicts.FileHasConflictMarkers(file.Path)
+				// Join with the refresh's repo root rather than relying on the
+				// process working directory, which may already point at another
+				// repo if the user switched while this refresh was in flight.
+				hasConflicts, err := mergeconflicts.FileHasConflictMarkers(
+					filepath.Join(env.git.RepoPaths.WorktreePath(), file.Path))
 				if err != nil {
 					self.c.Log.Error(err)
 				} else if !hasConflicts {