diff --git a/cmd/hook.go b/cmd/hook.go
index f38fd8831b8d5..77f8add8a5064 100644
--- a/cmd/hook.go
+++ b/cmd/hook.go
@@ -446,7 +446,7 @@ Gitea or set your environment appropriately.`, "")
 
 func hookPrintResults(results []private.HookPostReceiveBranchResult) {
 	for _, res := range results {
-		if !res.Message {
+		if !res.Message || res.Branch == "git-annex" || strings.HasPrefix(res.Branch, "synced/") {
 			continue
 		}
 
diff --git a/models/activities/action.go b/models/activities/action.go
index 15bd9a52acc5c..9b4bbf9193efd 100644
--- a/models/activities/action.go
+++ b/models/activities/action.go
@@ -559,6 +559,11 @@ func activityQueryCondition(ctx context.Context, opts GetFeedsOptions) (builder.
 		}
 	}
 
+	// Hide actions related to the git-annex branch
+	cond = cond.And(builder.Neq{"ref_name": git.BranchPrefix + "git-annex"})
+	// Hide actions related to git-annex's synced/* branches
+	cond = cond.And(builder.Not{builder.Like{"ref_name", git.BranchPrefix + "synced/%"}})
+
 	return cond, nil
 }
 
diff --git a/models/git/branch.go b/models/git/branch.go
index 6d50fb9fb6a18..72edcc37ede68 100644
--- a/models/git/branch.go
+++ b/models/git/branch.go
@@ -394,6 +394,8 @@ func FindRecentlyPushedNewBranches(ctx context.Context, repoID, userID int64, ex
 	err := db.GetEngine(ctx).
 		Where("pusher_id=? AND is_deleted=?", userID, false).
 		And("name <> ?", excludeBranchName).
+		And("name <> ?", "git-annex").
+		And("NOT name LIKE ?", "synced/%").
 		And("repo_id = ?", repoID).
 		And("commit_time >= ?", time.Now().Add(-time.Hour*6).Unix()).
 		NotIn("name", subQuery).
diff --git a/models/git/branch_list.go b/models/git/branch_list.go
index b5c1301a1dc00..2004abe8c7d02 100644
--- a/models/git/branch_list.go
+++ b/models/git/branch_list.go
@@ -79,6 +79,11 @@ func (opts *FindBranchOptions) Cond() builder.Cond {
 		cond = cond.And(builder.Eq{"repo_id": opts.RepoID})
 	}
 
+	// Hide the git-annex branch if it exists
+	cond = cond.And(builder.Neq{"name": "git-annex"})
+	// Hide synced/* branches that git-annex might have created
+	cond = cond.And(builder.Not{builder.Like{"name", "synced/%"}})
+
 	if len(opts.ExcludeBranchNames) > 0 {
 		cond = cond.And(builder.NotIn("name", opts.ExcludeBranchNames))
 	}
diff --git a/modules/annex/annex.go b/modules/annex/annex.go
index bb049d77ed686..af7fb7182dc97 100644
--- a/modules/annex/annex.go
+++ b/modules/annex/annex.go
@@ -152,3 +152,9 @@ func IsAnnexed(blob *git.Blob) (bool, error) {
 	}
 	return true, nil
 }
+
+// IsAnnexRepo determines if repo is a git-annex enabled repository
+func IsAnnexRepo(repo *git.Repository) bool {
+	_, _, err := git.NewCommand(repo.Ctx, "annex", "info").RunStdString(&git.RunOpts{Dir: repo.Path})
+	return err == nil
+}
diff --git a/routers/web/repo/branch.go b/routers/web/repo/branch.go
index bc72d5f2eca17..7090f0364e596 100644
--- a/routers/web/repo/branch.go
+++ b/routers/web/repo/branch.go
@@ -15,6 +15,7 @@ import (
 	git_model "code.gitea.io/gitea/models/git"
 	repo_model "code.gitea.io/gitea/models/repo"
 	"code.gitea.io/gitea/models/unit"
+	"code.gitea.io/gitea/modules/annex"
 	"code.gitea.io/gitea/modules/base"
 	"code.gitea.io/gitea/modules/context"
 	"code.gitea.io/gitea/modules/git"
@@ -45,6 +46,10 @@ func Branches(ctx *context.Context) {
 	ctx.Data["PageIsViewCode"] = true
 	ctx.Data["PageIsBranches"] = true
 
+	if annex.IsAnnexRepo(ctx.Repo.GitRepo) {
+		ctx.Flash.Info("This repository is a git-annex repository, the git-annex branch as well as all synced/* branches are hidden to avoid accidental changes to or from them.", true)
+	}
+
 	page := ctx.FormInt("page")
 	if page <= 1 {
 		page = 1
diff --git a/templates/repo/branch/list.tmpl b/templates/repo/branch/list.tmpl
index cec5b6fc3e62d..8314a58ad5c8c 100644
--- a/templates/repo/branch/list.tmpl
+++ b/templates/repo/branch/list.tmpl
@@ -1,5 +1,5 @@
 {{template "base/head" .}}
-<div role="main" aria-label="{{.Title}}" class="page-content ui repository branches">
+<div role="main" aria-label="{{.Title}}" class="page-content repository branches">
 	{{template "repo/header" .}}
 	<div class="ui container">
 		{{template "base/alert" .}}