diff --git a/internal/beads/beads.go b/internal/beads/beads.go
index 1ec4f2f6..6d09d56a 100644
--- a/internal/beads/beads.go
+++ b/internal/beads/beads.go
@@ -6,7 +6,9 @@ import (
 	"encoding/json"
 	"errors"
 	"fmt"
+	"os"
 	"os/exec"
+	"path/filepath"
 	"strings"
 	"time"
 )
@@ -1007,3 +1009,92 @@ func (b *Beads) GetAttachment(pinnedBeadID string) (*AttachmentFields, error) {
 func currentTimestamp() string {
 	return time.Now().UTC().Format(time.RFC3339)
 }
+
+// DetachAuditEntry represents an audit log entry for a detach operation.
+type DetachAuditEntry struct {
+	Timestamp        string `json:"timestamp"`
+	Operation        string `json:"operation"` // "detach", "burn", "squash"
+	PinnedBeadID     string `json:"pinned_bead_id"`
+	DetachedMolecule string `json:"detached_molecule"`
+	DetachedBy       string `json:"detached_by,omitempty"` // Agent that triggered detach
+	Reason           string `json:"reason,omitempty"`      // Optional reason for detach
+	PreviousState    string `json:"previous_state,omitempty"`
+}
+
+// DetachOptions specifies optional context for a detach operation.
+type DetachOptions struct {
+	Operation string // "detach", "burn", "squash" - defaults to "detach"
+	Agent     string // Who is performing the detach
+	Reason    string // Optional reason for the detach
+}
+
+// DetachMoleculeWithAudit removes molecule attachment from a pinned bead and logs the operation.
+// Returns the updated issue.
+func (b *Beads) DetachMoleculeWithAudit(pinnedBeadID string, opts DetachOptions) (*Issue, error) {
+	// Fetch the pinned bead first to get previous state
+	issue, err := b.Show(pinnedBeadID)
+	if err != nil {
+		return nil, fmt.Errorf("fetching pinned bead: %w", err)
+	}
+
+	// Get current attachment info for audit
+	attachment := ParseAttachmentFields(issue)
+	if attachment == nil {
+		return issue, nil // Nothing to detach
+	}
+
+	// Log the detach operation
+	operation := opts.Operation
+	if operation == "" {
+		operation = "detach"
+	}
+	entry := DetachAuditEntry{
+		Timestamp:        currentTimestamp(),
+		Operation:        operation,
+		PinnedBeadID:     pinnedBeadID,
+		DetachedMolecule: attachment.AttachedMolecule,
+		DetachedBy:       opts.Agent,
+		Reason:           opts.Reason,
+		PreviousState:    issue.Status,
+	}
+	if err := b.LogDetachAudit(entry); err != nil {
+		// Log error but don't fail the detach operation
+		fmt.Fprintf(os.Stderr, "Warning: failed to write audit log: %v\n", err)
+	}
+
+	// Clear attachment fields by passing nil
+	newDesc := SetAttachmentFields(issue, nil)
+
+	// Update the issue
+	if err := b.Update(pinnedBeadID, UpdateOptions{Description: &newDesc}); err != nil {
+		return nil, fmt.Errorf("updating pinned bead: %w", err)
+	}
+
+	// Re-fetch to return updated state
+	return b.Show(pinnedBeadID)
+}
+
+// LogDetachAudit appends an audit entry to the audit log file.
+// The audit log is stored in .beads/audit.log as JSONL format.
+func (b *Beads) LogDetachAudit(entry DetachAuditEntry) error {
+	auditPath := filepath.Join(b.workDir, ".beads", "audit.log")
+
+	// Marshal entry to JSON
+	data, err := json.Marshal(entry)
+	if err != nil {
+		return fmt.Errorf("marshaling audit entry: %w", err)
+	}
+
+	// Append to audit log file
+	f, err := os.OpenFile(auditPath, os.O_CREATE|os.O_APPEND|os.O_WRONLY, 0644)
+	if err != nil {
+		return fmt.Errorf("opening audit log: %w", err)
+	}
+	defer f.Close()
+
+	if _, err := f.Write(append(data, '\n')); err != nil {
+		return fmt.Errorf("writing audit entry: %w", err)
+	}
+
+	return nil
+}
diff --git a/internal/cmd/molecule_attach.go b/internal/cmd/molecule_attach.go
index 982ad3d6..b5731e8c 100644
--- a/internal/cmd/molecule_attach.go
+++ b/internal/cmd/molecule_attach.go
@@ -8,6 +8,7 @@ import (
 	"github.com/spf13/cobra"
 	"github.com/steveyegge/gastown/internal/beads"
 	"github.com/steveyegge/gastown/internal/style"
+	"github.com/steveyegge/gastown/internal/workspace"
 )
 
 func runMoleculeAttach(cmd *cobra.Command, args []string) error {
@@ -59,8 +60,11 @@ func runMoleculeDetach(cmd *cobra.Command, args []string) error {
 
 	previousMolecule := attachment.AttachedMolecule
 
-	// Detach the molecule
-	_, err = b.DetachMolecule(pinnedBeadID)
+	// Detach the molecule with audit logging
+	_, err = b.DetachMoleculeWithAudit(pinnedBeadID, beads.DetachOptions{
+		Operation: "detach",
+		Agent:     detectCurrentAgent(),
+	})
 	if err != nil {
 		return fmt.Errorf("detaching molecule: %w", err)
 	}
@@ -126,3 +130,20 @@ func runMoleculeAttachment(cmd *cobra.Command, args []string) error {
 
 	return nil
 }
+
+// detectCurrentAgent returns the current agent identity based on working directory.
+// Returns empty string if identity cannot be determined.
+func detectCurrentAgent() string {
+	cwd, err := os.Getwd()
+	if err != nil {
+		return ""
+	}
+
+	townRoot, err := workspace.FindFromCwd()
+	if err != nil || townRoot == "" {
+		return ""
+	}
+
+	ctx := detectRole(cwd, townRoot)
+	return buildAgentIdentity(ctx)
+}
diff --git a/internal/cmd/molecule_lifecycle.go b/internal/cmd/molecule_lifecycle.go
index 5a9b5676..79978544 100644
--- a/internal/cmd/molecule_lifecycle.go
+++ b/internal/cmd/molecule_lifecycle.go
@@ -201,8 +201,12 @@ func runMoleculeBurn(cmd *cobra.Command, args []string) error {
 
 	moleculeID := attachment.AttachedMolecule
 
-	// Detach the molecule (this "burns" it by removing the attachment)
-	_, err = b.DetachMolecule(handoff.ID)
+	// Detach the molecule with audit logging (this "burns" it by removing the attachment)
+	_, err = b.DetachMoleculeWithAudit(handoff.ID, beads.DetachOptions{
+		Operation: "burn",
+		Agent:     target,
+		Reason:    "molecule burned by agent",
+	})
 	if err != nil {
 		return fmt.Errorf("detaching molecule: %w", err)
 	}
@@ -334,8 +338,12 @@ squashed_at: %s
 			style.Dim.Render("Warning:"), err)
 	}
 
-	// Detach the molecule from the handoff bead
-	_, err = b.DetachMolecule(handoff.ID)
+	// Detach the molecule from the handoff bead with audit logging
+	_, err = b.DetachMoleculeWithAudit(handoff.ID, beads.DetachOptions{
+		Operation: "squash",
+		Agent:     target,
+		Reason:    fmt.Sprintf("molecule squashed to digest %s", digestIssue.ID),
+	})
 	if err != nil {
 		return fmt.Errorf("detaching molecule: %w", err)
 	}