diff --git a/pinning/pinner/dspinner/pin.go b/pinning/pinner/dspinner/pin.go
index c32a13db2..94c8a3dea 100644
--- a/pinning/pinner/dspinner/pin.go
+++ b/pinning/pinner/dspinner/pin.go
@@ -646,35 +646,9 @@ func (p *pinner) CheckIfPinnedWithType(ctx context.Context, mode ipfspinner.Mode
 
 		// Check for indirect pins
 		if toCheck.Len() > 0 {
-			var walkErr error
-			visited := cid.NewSet()
-			err := p.cidRIndex.ForEach(ctx, "", func(key, value string) bool {
-				var rk cid.Cid
-				rk, walkErr = cid.Cast([]byte(key))
-				if walkErr != nil {
-					return false
-				}
-				walkErr = merkledag.Walk(ctx, merkledag.GetLinksWithDAG(p.dserv), rk, func(c cid.Cid) bool {
-					if toCheck.Len() == 0 || !visited.Visit(c) {
-						return false
-					}
-					if toCheck.Has(c) {
-						pinned = append(pinned, ipfspinner.Pinned{Key: c, Mode: ipfspinner.Indirect, Via: rk})
-						toCheck.Remove(c)
-					}
-					return true
-				}, merkledag.Concurrent())
-				if walkErr != nil {
-					return false
-				}
-				return toCheck.Len() > 0
-			})
-			if err != nil {
+			if err := p.traverseIndirectPins(ctx, toCheck, &pinned); err != nil {
 				return nil, err
 			}
-			if walkErr != nil {
-				return nil, walkErr
-			}
 		}
 
 		// Anything left in toCheck is not pinned
@@ -741,48 +715,93 @@ func (p *pinner) checkPinsInIndex(ctx context.Context, mode ipfspinner.Mode, inc
 	return pinned, nil
 }
 
+// traverseIndirectPins is a helper that traverses all recursive pins to find indirect pins.
+// It modifies the pinned slice and toCheck set in place.
+func (p *pinner) traverseIndirectPins(ctx context.Context, toCheck *cid.Set, pinned *[]ipfspinner.Pinned) error {
+	var walkErr error
+	visited := cid.NewSet()
+	err := p.cidRIndex.ForEach(ctx, "", func(key, value string) bool {
+		// Check for context cancellation at the start of each recursive pin
+		select {
+		case <-ctx.Done():
+			walkErr = ctx.Err()
+			return false
+		default:
+		}
+
+		var rk cid.Cid
+		rk, walkErr = cid.Cast([]byte(key))
+		if walkErr != nil {
+			return false
+		}
+		walkErr = merkledag.Walk(ctx, merkledag.GetLinksWithDAG(p.dserv), rk, func(c cid.Cid) bool {
+			if toCheck.Len() == 0 || !visited.Visit(c) {
+				return false
+			}
+			if toCheck.Has(c) {
+				*pinned = append(*pinned, ipfspinner.Pinned{Key: c, Mode: ipfspinner.Indirect, Via: rk})
+				toCheck.Remove(c)
+			}
+			return true
+		}, merkledag.Concurrent())
+		if walkErr != nil {
+			return false
+		}
+		return toCheck.Len() > 0
+	})
+	if err != nil {
+		return err
+	}
+	if walkErr != nil {
+		return walkErr
+	}
+	return nil
+}
+
 // checkIndirectPins checks if the given cids are pinned indirectly
 func (p *pinner) checkIndirectPins(ctx context.Context, cids ...cid.Cid) ([]ipfspinner.Pinned, error) {
 	pinned := make([]ipfspinner.Pinned, 0, len(cids))
 	toCheck := cid.NewSet()
 
-	// Check all CIDs for indirect pins, regardless of their direct pin status
-	// A CID can be both directly pinned AND indirectly pinned through a parent
+	// Filter out CIDs that are recursively pinned at the root level.
+	// A recursively pinned CID is not considered indirect because recursive pins
+	// are comprehensive (include all children), making "recursive" take precedence
+	// over "indirect".
+	//
+	// However, we do NOT filter out direct pins here. Direct pins only pin a
+	// single block, not its children. Therefore, a CID can legitimately be both:
+	// - Directly pinned (explicitly pinned as a single block)
+	// - Indirectly pinned (referenced by another pinned object's DAG)
+	// This is why the asymmetry between recursive and direct pins is intentional.
+	//
+	// NOTE: While this behavior may feel arbitrary, we preserve it for compatibility
+	// as this is how 'ipfs pin ls' has behaved for nearly a decade. The test
+	// t0081-repo-pinning.sh in Kubo explicitly expects a CID to be both direct
+	// and indirect, guarding this established behavior.
 	for _, c := range cids {
+		cidKey := c.KeyString()
+
+		// Check if recursively pinned
+		ids, err := p.cidRIndex.Search(ctx, cidKey)
+		if err != nil {
+			return nil, err
+		}
+		if len(ids) > 0 {
+			// This CID is recursively pinned at root level, not indirect
+			pinned = append(pinned, ipfspinner.Pinned{Key: c, Mode: ipfspinner.NotPinned})
+			continue
+		}
+
+		// Still check for indirect even if directly pinned
+		// A CID can be both direct and indirect
 		toCheck.Add(c)
 	}
 
 	// Now check for indirect pins by traversing recursive pins
 	if toCheck.Len() > 0 {
-		var walkErr error
-		visited := cid.NewSet()
-		err := p.cidRIndex.ForEach(ctx, "", func(key, value string) bool {
-			var rk cid.Cid
-			rk, walkErr = cid.Cast([]byte(key))
-			if walkErr != nil {
-				return false
-			}
-			walkErr = merkledag.Walk(ctx, merkledag.GetLinksWithDAG(p.dserv), rk, func(c cid.Cid) bool {
-				if toCheck.Len() == 0 || !visited.Visit(c) {
-					return false
-				}
-				if toCheck.Has(c) {
-					pinned = append(pinned, ipfspinner.Pinned{Key: c, Mode: ipfspinner.Indirect, Via: rk})
-					toCheck.Remove(c)
-				}
-				return true
-			}, merkledag.Concurrent())
-			if walkErr != nil {
-				return false
-			}
-			return toCheck.Len() > 0
-		})
-		if err != nil {
+		if err := p.traverseIndirectPins(ctx, toCheck, &pinned); err != nil {
 			return nil, err
 		}
-		if walkErr != nil {
-			return nil, walkErr
-		}
 	}
 
 	// Anything left in toCheck is not pinned
diff --git a/pinning/pinner/dspinner/pin_withtype_test.go b/pinning/pinner/dspinner/pin_withtype_test.go
index a53809260..a5da52045 100644
--- a/pinning/pinner/dspinner/pin_withtype_test.go
+++ b/pinning/pinner/dspinner/pin_withtype_test.go
@@ -2,7 +2,9 @@ package dspinner
 
 import (
 	"context"
+	"fmt"
 	"testing"
+	"time"
 
 	bs "github.com/ipfs/boxo/blockservice"
 	blockstore "github.com/ipfs/boxo/blockstore"
@@ -155,4 +157,57 @@ func TestCheckIfPinnedWithType(t *testing.T) {
 
 		require.Equal(t, pinned1, pinned2)
 	})
+
+	t.Run("Context cancellation during indirect check with many pins", func(t *testing.T) {
+		// Create many recursive pins to ensure we can hit the cancellation
+		nodes := make([]cid.Cid, 50)
+		for i := 0; i < 50; i++ {
+			node := mdag.NodeWithData([]byte(fmt.Sprintf("recursive node %d", i)))
+			err = dserv.Add(ctx, node)
+			require.NoError(t, err)
+			nodes[i] = node.Cid()
+
+			p.PinWithMode(ctx, nodes[i], ipfspin.Recursive, fmt.Sprintf("recursive-%d", i))
+		}
+		err = p.Flush(ctx)
+		require.NoError(t, err)
+
+		// Create a context that we can cancel
+		cancelCtx, cancel := context.WithCancel(ctx)
+
+		// Start checking in a goroutine
+		done := make(chan struct{})
+		var checkErr error
+		go func() {
+			defer close(done)
+			// Try to check for an indirect pin with many recursive pins to traverse
+			_, checkErr = p.CheckIfPinnedWithType(cancelCtx, ipfspin.Indirect, withoutNames, ck)
+		}()
+
+		// Cancel the context quickly
+		time.Sleep(1 * time.Millisecond)
+		cancel()
+
+		// Wait for the check to complete
+		<-done
+
+		// Should get a context cancellation error (or nil if it completed too fast)
+		// The important thing is that it doesn't hang
+		if checkErr != nil {
+			require.Equal(t, context.Canceled, checkErr)
+		}
+	})
+
+	t.Run("Context cancellation in checkIndirectPins", func(t *testing.T) {
+		// Create a context that we can cancel immediately
+		cancelCtx, cancel := context.WithCancel(ctx)
+		cancel() // Cancel immediately
+
+		// Try to check for indirect pins with cancelled context
+		_, err = p.CheckIfPinnedWithType(cancelCtx, ipfspin.Indirect, withoutNames, ck)
+
+		// Should get a context cancellation error
+		require.Error(t, err)
+		require.Equal(t, context.Canceled, err)
+	})
 }