diff --git a/internal/devconfig/config_test.go b/internal/devconfig/config_test.go
index 9f747796156..f7152eec384 100644
--- a/internal/devconfig/config_test.go
+++ b/internal/devconfig/config_test.go
@@ -1,6 +1,7 @@
 package devconfig
 
 import (
+	"fmt"
 	"io/fs"
 	"os"
 	"path/filepath"
@@ -430,6 +431,34 @@ func TestDefault(t *testing.T) {
 	}
 }
 
+// TestPackagesDoesNotDedupDistinctGitFlakes is a regression test for issue
+// #2704. Two git flake references that point at the same repository but
+// different subdirectories (via the "dir" query parameter) are distinct
+// inputs and must both be preserved by Config.Packages(). Previously they
+// were deduplicated because the "@" in the "git@host" portion of the URL was
+// mistaken for a version delimiter, giving both packages the same parsed name.
+func TestPackagesDoesNotDedupDistinctGitFlakes(t *testing.T) {
+	pkgA := "git+ssh://git@gitlab.com/org/repo.git?dir=betteralign&ref=master&rev=17d2bedca4884176e0d08078aa42311053e531c2"
+	pkgB := "git+ssh://git@gitlab.com/org/repo.git?dir=recovergoroutine&ref=master&rev=593d44945851d912f0c2158c46cc76da445adc43"
+
+	jsonConfig := fmt.Sprintf(`{"packages":[%q,%q]}`, pkgA, pkgB)
+	cfg, err := loadBytes([]byte(jsonConfig))
+	if err != nil {
+		t.Fatalf("load error: %v", err)
+	}
+
+	packages := cfg.Packages(false /*includeRemovedTriggerPackages*/)
+	got := make([]string, len(packages))
+	for i, p := range packages {
+		got[i] = p.VersionedName()
+	}
+
+	want := []string{pkgA, pkgB}
+	if diff := cmp.Diff(want, got); diff != "" {
+		t.Errorf("Config.Packages() dropped a distinct git flake input (-want +got):\n%s", diff)
+	}
+}
+
 func TestOSExpandIfPossible(t *testing.T) {
 	tests := []struct {
 		name        string
diff --git a/internal/devconfig/configfile/packages.go b/internal/devconfig/configfile/packages.go
index 2c445d33d1d..3589af0e66b 100644
--- a/internal/devconfig/configfile/packages.go
+++ b/internal/devconfig/configfile/packages.go
@@ -11,6 +11,7 @@ import (
 	"github.com/pkg/errors"
 	orderedmap "github.com/wk8/go-ordered-map/v2"
 	"go.jetify.com/devbox/internal/boxcli/usererr"
+	"go.jetify.com/devbox/internal/devpkg/pkgtype"
 	"go.jetify.com/devbox/internal/nix"
 	"go.jetify.com/devbox/internal/searcher"
 	"go.jetify.com/devbox/internal/ux"
@@ -361,6 +362,17 @@ func (p *Package) UnmarshalJSON(data []byte) error {
 
 // parseVersionedName parses the name and version from package@version representation
 func parseVersionedName(versionedName string) (name, version string) {
+	// Flake references are not versioned Devbox packages, and they may
+	// legitimately contain an "@" in their URL (for example
+	// "git+ssh://git@gitlab.com/org/repo.git?dir=foo"). Splitting such a
+	// reference on "@" produces a name that is not unique across flakes that
+	// differ only by their query parameters (such as "dir"), which causes
+	// distinct inputs to be incorrectly deduplicated. Treat the whole
+	// reference as the name in that case. See issue #2704.
+	if pkgtype.IsFlake(versionedName) {
+		return versionedName, "" /*version*/
+	}
+
 	var found bool
 	name, version, found = searcher.ParseVersionedPackage(versionedName)
 	if !found {
diff --git a/internal/devconfig/configfile/packages_test.go b/internal/devconfig/configfile/packages_test.go
index 38aefa46cd0..0f2d3c20cda 100644
--- a/internal/devconfig/configfile/packages_test.go
+++ b/internal/devconfig/configfile/packages_test.go
@@ -288,6 +288,22 @@ func TestParseVersionedName(t *testing.T) {
 			expectedName:    "github:nixos/nixpkgs/5233fd2ba76a3accb5aaa999c00509a11fd0793c#hello",
 			expectedVersion: "",
 		},
+		{
+			// Git flake refs contain "@" in their URL (git@host) but are
+			// not versioned packages. The whole ref must be the name so
+			// that refs differing only by query params (e.g. "dir") stay
+			// distinct. See issue #2704.
+			name:            "git-ssh-flake-with-dir",
+			input:           "git+ssh://git@gitlab.com/org/repo.git?dir=betteralign&ref=master&rev=17d2bedca4884176e0d08078aa42311053e531c2",
+			expectedName:    "git+ssh://git@gitlab.com/org/repo.git?dir=betteralign&ref=master&rev=17d2bedca4884176e0d08078aa42311053e531c2",
+			expectedVersion: "",
+		},
+		{
+			name:            "git-ssh-flake-without-query",
+			input:           "git+ssh://git@github.com/org/repo.git",
+			expectedName:    "git+ssh://git@github.com/org/repo.git",
+			expectedVersion: "",
+		},
 	}
 
 	for _, testCase := range testCases {