diff --git a/cmd/ceremony/main.go b/cmd/ceremony/main.go
index 0ee69aa9fb7..1a8a390457f 100644
--- a/cmd/ceremony/main.go
+++ b/cmd/ceremony/main.go
@@ -94,10 +94,14 @@ func postIssuanceLinting(fc, issuer, existing *x509.Certificate, skipLints []str
 	if err != nil {
 		return fmt.Errorf("unable to create lint config: %s", err)
 	}
-	registry, err := linter.NewRegistryWithConfig(skipLints, lintConfig)
+	registry, err := linter.NewRegistry(skipLints)
 	if err != nil {
 		return fmt.Errorf("unable to create zlint registry: %s", err)
 	}
+	registry, err = linter.ConfigureRegistry(registry, lintConfig)
+	if err != nil {
+		return fmt.Errorf("unable to configure zlint registry: %s", err)
+	}
 	lintRes := zlint.LintCertificateEx(parsed, registry)
 	err = linter.ProcessResultSet(lintRes)
 	if err != nil {
diff --git a/cmd/cert-checker/main.go b/cmd/cert-checker/main.go
index 4e8ba80aa56..e327df76828 100644
--- a/cmd/cert-checker/main.go
+++ b/cmd/cert-checker/main.go
@@ -32,6 +32,7 @@ import (
 	"github.com/letsencrypt/boulder/goodkey"
 	"github.com/letsencrypt/boulder/goodkey/sagoodkey"
 	"github.com/letsencrypt/boulder/identifier"
+	"github.com/letsencrypt/boulder/issuance"
 	"github.com/letsencrypt/boulder/linter"
 	blog "github.com/letsencrypt/boulder/log"
 	"github.com/letsencrypt/boulder/policy"
@@ -125,7 +126,9 @@ type certChecker struct {
 	issuedReport                report
 	checkPeriod                 time.Duration
 	acceptableValidityDurations map[time.Duration]bool
+	issuers                     map[string]*issuance.Certificate
 	lints                       lint.Registry
+	lintConfig                  linter.Config
 	logger                      blog.Logger
 }
 
@@ -135,7 +138,9 @@ func newChecker(saDbMap certDB,
 	kp goodkey.KeyPolicy,
 	period time.Duration,
 	avd map[time.Duration]bool,
+	issuers map[string]*issuance.Certificate,
 	lints lint.Registry,
+	lintConfig linter.Config,
 	logger blog.Logger,
 ) certChecker {
 	precertGetter := func(ctx context.Context, serial string) ([]byte, error) {
@@ -154,7 +159,9 @@ func newChecker(saDbMap certDB,
 		clock:                       clk,
 		checkPeriod:                 period,
 		acceptableValidityDurations: avd,
+		issuers:                     issuers,
 		lints:                       lints,
+		lintConfig:                  lintConfig,
 		logger:                      logger,
 	}
 }
@@ -373,8 +380,29 @@ func (c *certChecker) checkCert(ctx context.Context, cert *corepb.Certificate) (
 		sans = append(sans, ip.String())
 	}
 
+	// Configure zlint.
+	lintConfig := c.lintConfig
+	if len(c.issuers) > 0 {
+		issuer, ok := c.issuers[parsedCert.Issuer.CommonName]
+		if !ok {
+			problems = append(problems, fmt.Sprintf("Unrecognized issuer: %q", parsedCert.Issuer.CommonName))
+			return nil, problems
+		}
+
+		lintConfig, err = c.lintConfig.WithIssuer(issuer.Certificate)
+		if err != nil {
+			problems = append(problems, "Couldn't configure lints with issuer")
+			return nil, problems
+		}
+	}
+	registry, err := linter.ConfigureRegistry(c.lints, lintConfig)
+	if err != nil {
+		problems = append(problems, "Couldn't create lint registry")
+		return nil, problems
+	}
+
 	// Run zlint checks.
-	results := zlint.LintCertificateEx(parsedCert, c.lints)
+	results := zlint.LintCertificateEx(parsedCert, registry)
 	for name, res := range results.Results {
 		if res.Status <= lint.Pass {
 			continue
@@ -592,6 +620,12 @@ type Config struct {
 		// configured to submit SCTs to test logs.
 		CTIncludeTestLogs bool
 
+		// IssuerCerts are paths to all intermediate certificates which may have
+		// been used to issue certificates in the last 90 days. These are used to
+		// configure our CP/CPS-specific lints.
+		// TODO(#5492): Change this to `"min=1,dive,required"`
+		IssuerCerts []string `validate:"omitempty"`
+
 		Features features.Config
 	}
 	PA     cmd.PAConfig
@@ -699,10 +733,18 @@ func main() {
 
 	lints, err := linter.NewRegistry(config.CertChecker.IgnoredLints)
 	cmd.FailOnError(err, "Failed to create zlint registry")
+
+	lintConfig := linter.Config{}
 	if config.CertChecker.LintConfig != "" {
-		lintconfig, err := lint.NewConfigFromFile(config.CertChecker.LintConfig)
+		lintConfig, err = linter.LoadConfigFile(config.CertChecker.LintConfig)
 		cmd.FailOnError(err, "Failed to load zlint config file")
-		lints.SetConfiguration(lintconfig)
+	}
+
+	issuers := make(map[string]*issuance.Certificate)
+	for _, issuerCertPath := range config.CertChecker.IssuerCerts {
+		issuer, err := issuance.LoadCertificate(issuerCertPath)
+		cmd.FailOnError(err, "Failed to load issuer cert file")
+		issuers[issuer.Subject.CommonName] = issuer
 	}
 
 	checker := newChecker(
@@ -712,7 +754,9 @@ func main() {
 		kp,
 		config.CertChecker.CheckPeriod.Duration,
 		acceptableValidityDurations,
+		issuers,
 		lints,
+		lintConfig,
 		logger,
 	)
 	fmt.Fprintf(os.Stderr, "# Getting certificates issued in the last %s\n", config.CertChecker.CheckPeriod)
diff --git a/cmd/cert-checker/main_test.go b/cmd/cert-checker/main_test.go
index 47d49994d33..9721e164ce5 100644
--- a/cmd/cert-checker/main_test.go
+++ b/cmd/cert-checker/main_test.go
@@ -72,7 +72,7 @@ func init() {
 }
 
 func BenchmarkCheckCert(b *testing.B) {
-	checker := newChecker(nil, clock.New(), pa, kp, time.Hour, testValidityDurations, nil, blog.NewMock())
+	checker := newChecker(nil, clock.New(), pa, kp, time.Hour, testValidityDurations, nil, nil, linter.Config{}, blog.NewMock())
 	testKey, _ := ecdsa.GenerateKey(elliptic.P256(), rand.Reader)
 	expiry := time.Now().AddDate(0, 0, 1)
 	serial := big.NewInt(1337)
@@ -108,7 +108,7 @@ func TestCheckWildcardCert(t *testing.T) {
 
 	testKey, _ := rsa.GenerateKey(rand.Reader, 2048)
 	fc := clock.NewFake()
-	checker := newChecker(saDbMap, fc, pa, kp, time.Hour, testValidityDurations, nil, blog.NewMock())
+	checker := newChecker(saDbMap, fc, pa, kp, time.Hour, testValidityDurations, nil, nil, linter.Config{}, blog.NewMock())
 	issued := checker.clock.Now().Add(-time.Minute)
 	goodExpiry := issued.Add(testValidityDuration - time.Second)
 	serial := big.NewInt(1337)
@@ -151,7 +151,7 @@ func TestCheckCertReturnsSANs(t *testing.T) {
 	defer func() {
 		saCleanup()
 	}()
-	checker := newChecker(saDbMap, clock.NewFake(), pa, kp, time.Hour, testValidityDurations, nil, blog.NewMock())
+	checker := newChecker(saDbMap, clock.NewFake(), pa, kp, time.Hour, testValidityDurations, nil, nil, linter.Config{}, blog.NewMock())
 
 	certPEM, err := os.ReadFile("testdata/quite_invalid.pem")
 	if err != nil {
@@ -218,7 +218,7 @@ func TestCheckCert(t *testing.T) {
 		t.Run(tc.name, func(t *testing.T) {
 			testKey, _ := tc.key.genKey()
 
-			checker := newChecker(saDbMap, clock.NewFake(), pa, kp, time.Hour, testValidityDurations, nil, blog.NewMock())
+			checker := newChecker(saDbMap, clock.NewFake(), pa, kp, time.Hour, testValidityDurations, nil, nil, linter.Config{}, blog.NewMock())
 
 			// Create a RFC 7633 OCSP Must Staple Extension.
 			// OID 1.3.6.1.5.5.7.1.24
@@ -340,7 +340,7 @@ func TestGetAndProcessCerts(t *testing.T) {
 	fc.Set(fc.Now().Add(time.Hour))
 
 	mocklog := blog.NewMock()
-	checker := newChecker(saDbMap, fc, pa, kp, time.Hour, testValidityDurations, nil, mocklog)
+	checker := newChecker(saDbMap, fc, pa, kp, time.Hour, testValidityDurations, nil, nil, linter.Config{}, mocklog)
 	sa, err := sa.NewSQLStorageAuthority(saDbMap, saDbMap, nil, 0, fc, blog.NewMock(), metrics.NoopRegisterer)
 	test.AssertNotError(t, err, "Couldn't create SA to insert certificates")
 	saCleanUp := test.ResetBoulderTestDatabase(t)
@@ -426,7 +426,7 @@ func (db mismatchedCountDB) SelectOne(_ context.Context, holder any, _ string, _
 func TestGetCertsEmptyResults(t *testing.T) {
 	saDbMap, err := sa.DBMapForTest(vars.DBConnSA)
 	test.AssertNotError(t, err, "Couldn't connect to database")
-	checker := newChecker(saDbMap, clock.NewFake(), pa, kp, time.Hour, testValidityDurations, nil, blog.NewMock())
+	checker := newChecker(saDbMap, clock.NewFake(), pa, kp, time.Hour, testValidityDurations, nil, nil, linter.Config{}, blog.NewMock())
 	checker.dbMap = mismatchedCountDB{}
 
 	batchSize = 3
@@ -453,7 +453,7 @@ func (db emptyDB) SelectOne(_ context.Context, holder any, _ string, _ ...any) e
 // expected if the DB finds no certificates to match the SELECT query and
 // should return an error.
 func TestGetCertsNullResults(t *testing.T) {
-	checker := newChecker(emptyDB{}, clock.NewFake(), pa, kp, time.Hour, testValidityDurations, nil, blog.NewMock())
+	checker := newChecker(emptyDB{}, clock.NewFake(), pa, kp, time.Hour, testValidityDurations, nil, nil, linter.Config{}, blog.NewMock())
 
 	err := checker.getCerts(context.Background())
 	test.AssertError(t, err, "Should have gotten error from empty DB")
@@ -499,7 +499,7 @@ func TestGetCertsLate(t *testing.T) {
 	clk := clock.NewFake()
 	db := &lateDB{issuedTime: clk.Now().Add(-time.Hour)}
 	checkPeriod := 24 * time.Hour
-	checker := newChecker(db, clk, pa, kp, checkPeriod, testValidityDurations, nil, blog.NewMock())
+	checker := newChecker(db, clk, pa, kp, checkPeriod, testValidityDurations, nil, nil, linter.Config{}, blog.NewMock())
 
 	err := checker.getCerts(context.Background())
 	test.AssertNotError(t, err, "getting certs")
@@ -560,7 +560,7 @@ func TestIgnoredLint(t *testing.T) {
 	err = loglist.InitLintList("../../test/ct-test-srv/log_list.json", false)
 	test.AssertNotError(t, err, "failed to load ct log list")
 	testKey, _ := rsa.GenerateKey(rand.Reader, 2048)
-	checker := newChecker(saDbMap, clock.NewFake(), pa, kp, time.Hour, testValidityDurations, nil, blog.NewMock())
+	checker := newChecker(saDbMap, clock.NewFake(), pa, kp, time.Hour, testValidityDurations, nil, nil, linter.Config{}, blog.NewMock())
 	serial := big.NewInt(1337)
 
 	x509OID, err := x509.OIDFromInts([]uint64{1, 2, 3})
@@ -642,7 +642,7 @@ func TestIgnoredLint(t *testing.T) {
 }
 
 func TestPrecertCorrespond(t *testing.T) {
-	checker := newChecker(nil, clock.New(), pa, kp, time.Hour, testValidityDurations, nil, blog.NewMock())
+	checker := newChecker(nil, clock.New(), pa, kp, time.Hour, testValidityDurations, nil, nil, linter.Config{}, blog.NewMock())
 	checker.getPrecert = func(_ context.Context, _ string) ([]byte, error) {
 		return []byte("hello"), nil
 	}
diff --git a/linter/config.go b/linter/config.go
index 4e49e99c7a4..6ea5da03c96 100644
--- a/linter/config.go
+++ b/linter/config.go
@@ -106,12 +106,15 @@ func (r configuredRegistry) GetConfiguration() lint.Configuration {
 	return r.config
 }
 
-// NewRegistryWithConfig is like NewRegistry, but the returned registry also
-// carries the contents of the given Config.
-func NewRegistryWithConfig(skipLints []string, config Config) (lint.Registry, error) {
-	reg, err := NewRegistry(skipLints)
-	if err != nil {
-		return nil, err
+// ConfigureRegistry combines the given registry with the given config. This is
+// useful for reusing the same registry (which can be expensive to build) with
+// many different configs.
+func ConfigureRegistry(reg lint.Registry, config Config) (lint.Registry, error) {
+	if reg == nil {
+		// Normally zlint would replace a nil registry with the global registry on
+		// its own, but of course a configuredRegistry *isn't* nil even if the
+		// registry it wraps is, so we need to do this fallback ourselves.
+		reg = lint.GlobalRegistry()
 	}
 	lintConfig, err := config.build()
 	if err != nil {
diff --git a/test/config-next/cert-checker.json b/test/config-next/cert-checker.json
index e046cccc08c..6c463003a14 100644
--- a/test/config-next/cert-checker.json
+++ b/test/config-next/cert-checker.json
@@ -14,6 +14,14 @@
 			"1080h",
 			"160h"
 		],
+		"issuerCerts": [
+			"test/certs/webpki/int-rsa-a.cert.pem",
+			"test/certs/webpki/int-rsa-b.cert.pem",
+			"test/certs/webpki/int-rsa-c.cert.pem",
+			"test/certs/webpki/int-ecdsa-a.cert.pem",
+			"test/certs/webpki/int-ecdsa-b.cert.pem",
+			"test/certs/webpki/int-ecdsa-c.cert.pem"
+		],
 		"lintConfig": "test/config-next/zlint.toml",
 		"ignoredLints": [
 			"w_ext_subject_key_identifier_missing_sub_cert",