diff --git a/signature/algorithm.go b/signature/algorithm.go
index 83eea104..8e391924 100644
--- a/signature/algorithm.go
+++ b/signature/algorithm.go
@@ -26,7 +26,7 @@ type Algorithm int
 
 // Signature algorithms supported by this library.
 //
-// Reference: https://github.com/notaryproject/notaryproject/blob/main/signature-specification.md#algorithm-selection
+// Reference: https://github.com/notaryproject/notaryproject/blob/main/specs/signature-specification.md#algorithm-selection
 const (
 	AlgorithmPS256 Algorithm = 1 + iota // RSASSA-PSS with SHA-256
 	AlgorithmPS384                      // RSASSA-PSS with SHA-384
diff --git a/signature/internal/base/envelope.go b/signature/internal/base/envelope.go
index 5dbf24f5..41c685e0 100644
--- a/signature/internal/base/envelope.go
+++ b/signature/internal/base/envelope.go
@@ -33,7 +33,7 @@ type Envelope struct {
 
 // Sign generates signature in terms of given SignRequest.
 //
-// Reference: https://github.com/notaryproject/notaryproject/blob/main/signing-and-verification-workflow.md#signing-steps
+// Reference: https://github.com/notaryproject/notaryproject/blob/main/specs/signing-and-verification-workflow.md#signing-steps
 func (e *Envelope) Sign(req *signature.SignRequest) ([]byte, error) {
 	// Canonicalize request.
 	req.SigningTime = req.SigningTime.Truncate(time.Second)
@@ -71,7 +71,7 @@ func (e *Envelope) Sign(req *signature.SignRequest) ([]byte, error) {
 // It returns envelope content containing the payload to be signed and
 // SignerInfo object containing the information about the signature.
 //
-// Reference: https://github.com/notaryproject/notaryproject/blob/main/trust-store-trust-policy-specification.md#steps
+// Reference: https://github.com/notaryproject/notaryproject/blob/main/specs/trust-store-trust-policy.md#steps
 func (e *Envelope) Verify() (*signature.EnvelopeContent, error) {
 	// validation before the core verify process.
 	if len(e.Raw) == 0 {
diff --git a/signature/jws/types.go b/signature/jws/types.go
index 2c15b7e2..bfbb204b 100644
--- a/signature/jws/types.go
+++ b/signature/jws/types.go
@@ -31,7 +31,7 @@ const (
 )
 
 // headerKeys includes all system aware keys for JWS protected header
-// [JWS envelope]: https://github.com/notaryproject/notaryproject/blob/main/signature-envelope-jws.md#protected-headers
+// [JWS envelope]: https://github.com/notaryproject/notaryproject/blob/main/specs/signature-envelope-jws.md#protected-headers
 var headerKeys = []string{
 	headerKeyAlg,
 	headerKeyCty,
diff --git a/signature/signer.go b/signature/signer.go
index 692616e4..28053a38 100644
--- a/signature/signer.go
+++ b/signature/signer.go
@@ -126,7 +126,7 @@ func (s *localSigner) PrivateKey() crypto.PrivateKey {
 // with one of the trusted certificates and returns a certificate that matches
 // with one of the certificates in the SignerInfo.
 //
-// Reference: https://github.com/notaryproject/notaryproject/blob/main/trust-store-trust-policy-specification.md#steps
+// Reference: https://github.com/notaryproject/notaryproject/blob/main/specs/trust-store-trust-policy.md#steps
 func VerifyAuthenticity(signerInfo *SignerInfo, trustedCerts []*x509.Certificate) (*x509.Certificate, error) {
 	if len(trustedCerts) == 0 {
 		return nil, &InvalidArgumentError{Param: "trustedCerts"}
diff --git a/signature/types.go b/signature/types.go
index be51b091..e324b92f 100644
--- a/signature/types.go
+++ b/signature/types.go
@@ -24,7 +24,7 @@ type SignatureMediaType string
 
 // SigningScheme formalizes the feature set (guarantees) provided by
 // the signature.
-// Reference: https://github.com/notaryproject/notaryproject/blob/main/signing-scheme.md
+// Reference: https://github.com/notaryproject/notaryproject/blob/main/specs/signing-scheme.md
 type SigningScheme string
 
 // SigningSchemes supported by notation.
@@ -37,7 +37,7 @@ const (
 )
 
 // SignedAttributes represents signed metadata in the signature envelope.
-// Reference: https://github.com/notaryproject/notaryproject/blob/main/signature-specification.md#signed-attributes
+// Reference: https://github.com/notaryproject/notaryproject/blob/main/specs/signature-specification.md#signed-attributes
 type SignedAttributes struct {
 	// SigningScheme defines the Notary Project Signing Scheme used by the signature.
 	SigningScheme SigningScheme
@@ -53,7 +53,7 @@ type SignedAttributes struct {
 }
 
 // UnsignedAttributes represents unsigned metadata in the Signature envelope.
-// Reference: https://github.com/notaryproject/notaryproject/blob/main/signature-specification.md#unsigned-attributes
+// Reference: https://github.com/notaryproject/notaryproject/blob/main/specs/signature-specification.md#unsigned-attributes
 type UnsignedAttributes struct {
 	// TimestampSignature is a counter signature providing authentic timestamp.
 	TimestampSignature []byte
diff --git a/x509/cert_validations.go b/x509/cert_validations.go
index 28b998d2..84ba24dd 100644
--- a/x509/cert_validations.go
+++ b/x509/cert_validations.go
@@ -37,7 +37,7 @@ var kuLeafCertBlockedString = "ContentCommitment, KeyEncipherment, DataEncipherm
 // ValidateCodeSigningCertChain takes an ordered code-signing certificate chain
 // and validates issuance from leaf to root
 // Validates certificates according to this spec:
-// https://github.com/notaryproject/notaryproject/blob/main/signature-specification.md#certificate-requirements
+// https://github.com/notaryproject/notaryproject/blob/main/specs/signature-specification.md#certificate-requirements
 func ValidateCodeSigningCertChain(certChain []*x509.Certificate, signingTime *time.Time) error {
 	return validateCertChain(certChain, 0, signingTime)
 }
@@ -45,7 +45,7 @@ func ValidateCodeSigningCertChain(certChain []*x509.Certificate, signingTime *ti
 // ValidateTimeStampingCertChain takes an ordered time-stamping certificate
 // chain and validates issuance from leaf to root
 // Validates certificates according to this spec:
-// https://github.com/notaryproject/notaryproject/blob/main/signature-specification.md#certificate-requirements
+// https://github.com/notaryproject/notaryproject/blob/main/specs/signature-specification.md#certificate-requirements
 func ValidateTimeStampingCertChain(certChain []*x509.Certificate, signingTime *time.Time) error {
 	return validateCertChain(certChain, x509.ExtKeyUsageTimeStamping, signingTime)
 }