diff --git a/model/scanner.go b/model/scanner.go
index 54f81037c..36c9007fb 100644
--- a/model/scanner.go
+++ b/model/scanner.go
@@ -12,7 +12,7 @@ import (
 // NOTE: This struct is used as a map key, so it should only contain comparable types.
 type ScanTarget struct {
 	LibraryID  int
-	FolderPath string // Relative path within the library, or "" for entire library
+	FolderPath string // Path within the library (relative or absolute), or "" for entire library
 }
 
 func (st ScanTarget) String() string {
diff --git a/scanner/scanner.go b/scanner/scanner.go
index 29a1f9b4e..d73007bdd 100644
--- a/scanner/scanner.go
+++ b/scanner/scanner.go
@@ -4,6 +4,7 @@ import (
 	"context"
 	"fmt"
 	"maps"
+	"path/filepath"
 	"slices"
 	"sync/atomic"
 	"time"
@@ -51,6 +52,27 @@ func (s *scanState) sendError(err error) {
 	s.sendProgress(&ProgressInfo{Error: err.Error()})
 }
 
+// libraryRelativePath rebases an absolute scan target path onto the library root, since the
+// scanner's fs.FS only accepts paths relative to it. Relative paths, and absolute paths outside
+// the library root, are returned unchanged.
+func libraryRelativePath(libPath, folderPath string) string {
+	if !filepath.IsAbs(folderPath) {
+		return folderPath
+	}
+	// The library root may be relative (e.g. the default "./music"); it must be made absolute
+	// to match against an absolute target, and it resolves against the same cwd as the scanner's fs.
+	absLib, err := filepath.Abs(libPath)
+	if err != nil {
+		return folderPath
+	}
+	rel, err := filepath.Rel(absLib, folderPath)
+	if err != nil || !filepath.IsLocal(rel) {
+		return folderPath
+	}
+	// The scanner's fs.FS is an io/fs, which always uses forward slashes.
+	return filepath.ToSlash(rel)
+}
+
 func (s *scannerImpl) scanFolders(ctx context.Context, fullScan bool, targets []model.ScanTarget, progress chan<- *ProgressInfo) {
 	startTime := time.Now()
 
@@ -77,8 +99,12 @@ func (s *scannerImpl) scanFolders(ctx context.Context, fullScan bool, targets []
 		// Selective scan: filter libraries and build targets map
 		state.targets = make(map[int][]string)
 
+		libPaths := slice.ToMap(allLibs, func(lib model.Library) (int, string) {
+			return lib.ID, lib.Path
+		})
+
 		for _, target := range targets {
-			folderPath := target.FolderPath
+			folderPath := libraryRelativePath(libPaths[target.LibraryID], target.FolderPath)
 			if folderPath == "" {
 				folderPath = "."
 			}
diff --git a/scanner/scanner_internal_test.go b/scanner/scanner_internal_test.go
index e8abb7c7d..0778bd6ec 100644
--- a/scanner/scanner_internal_test.go
+++ b/scanner/scanner_internal_test.go
@@ -4,6 +4,8 @@ package scanner
 import (
 	"context"
 	"errors"
+	"os"
+	"path/filepath"
 	"sync/atomic"
 
 	ppl "github.com/google/go-pipeline/pkg/pipeline"
@@ -11,6 +13,43 @@ import (
 	. "github.com/onsi/gomega"
 )
 
+var _ = Describe("libraryRelativePath", func() {
+	// Paths are built with filepath so the "absolute" cases stay absolute on every OS
+	// (a Unix-style "/foo" is not absolute on Windows).
+	libRoot, _ := filepath.Abs(filepath.Join("jukebox", "collection"))
+	outside, _ := filepath.Abs(filepath.Join("somewhere", "else"))
+
+	It("returns a relative path unchanged", func() {
+		Expect(libraryRelativePath(libRoot, "_Collection")).To(Equal("_Collection"))
+	})
+
+	It("rebases an absolute target when the library root is relative", func() {
+		cwd, err := os.Getwd()
+		Expect(err).ToNot(HaveOccurred())
+		Expect(libraryRelativePath(filepath.Join("music", "library"), filepath.Join(cwd, "music", "library", "rock"))).To(Equal("rock"))
+	})
+
+	It("rebases an absolute path that equals the library root to '.'", func() {
+		Expect(libraryRelativePath(libRoot, libRoot)).To(Equal("."))
+	})
+
+	It("rebases an absolute path under the library root", func() {
+		Expect(libraryRelativePath(libRoot, filepath.Join(libRoot, "_Collection"))).To(Equal("_Collection"))
+	})
+
+	It("handles a trailing slash on the library path", func() {
+		Expect(libraryRelativePath(libRoot+string(filepath.Separator), filepath.Join(libRoot, "_Collection"))).To(Equal("_Collection"))
+	})
+
+	It("leaves an absolute path outside the library root unchanged", func() {
+		Expect(libraryRelativePath(libRoot, outside)).To(Equal(outside))
+	})
+
+	It("returns an empty path unchanged", func() {
+		Expect(libraryRelativePath(libRoot, "")).To(Equal(""))
+	})
+})
+
 type mockPhase struct {
 	num           int
 	produceFunc   func() ppl.Producer[int]