diff --git a/command/agent/consul/catalog_testing.go b/command/agent/consul/catalog_testing.go
index 61e5e3088..c087f024c 100644
--- a/command/agent/consul/catalog_testing.go
+++ b/command/agent/consul/catalog_testing.go
@@ -187,6 +187,12 @@ func (c *MockAgent) ServiceDeregister(serviceID string) error {
 	defer c.mu.Unlock()
 	c.hits++
 	delete(c.services, serviceID)
+	for k, v := range c.checks {
+		if v.ServiceID == serviceID {
+			delete(c.checks, k)
+			delete(c.checkTTLs, k)
+		}
+	}
 	return nil
 }
 
diff --git a/command/agent/consul/client.go b/command/agent/consul/client.go
index 645e907fd..ca93249b9 100644
--- a/command/agent/consul/client.go
+++ b/command/agent/consul/client.go
@@ -591,12 +591,6 @@ func (c *ServiceClient) sync(reason syncReason) error {
 		return fmt.Errorf("error querying Consul services: %v", err)
 	}
 
-	consulChecks, err := c.client.Checks()
-	if err != nil {
-		metrics.IncrCounter([]string{"client", "consul", "sync_failure"}, 1)
-		return fmt.Errorf("error querying Consul checks: %v", err)
-	}
-
 	inProbation := time.Now().Before(c.deregisterProbationExpiry)
 
 	// Remove Nomad services in Consul but unknown locally
@@ -656,6 +650,12 @@ func (c *ServiceClient) sync(reason syncReason) error {
 
 	}
 
+	consulChecks, err := c.client.Checks()
+	if err != nil {
+		metrics.IncrCounter([]string{"client", "consul", "sync_failure"}, 1)
+		return fmt.Errorf("error querying Consul checks: %v", err)
+	}
+
 	// Remove Nomad checks in Consul but unknown locally
 	for id, check := range consulChecks {
 		if _, ok := c.checks[id]; ok {
@@ -1227,9 +1227,28 @@ func (c *ServiceClient) Shutdown() error {
 			c.logger.Error("failed deregistering agent service", "service_id", id, "error", err)
 		}
 	}
+
+	remainingChecks, err := c.client.Checks()
+	if err != nil {
+		c.logger.Error("failed listing remaining checks after deregistering services", "error", err)
+	}
+
+	checkRemains := func(id string) bool {
+		for _, c := range remainingChecks {
+			if c.CheckID == id {
+				return true
+			}
+		}
+		return false
+	}
+
 	for id := range c.agentChecks {
-		if err := c.client.CheckDeregister(id); err != nil {
-			c.logger.Error("failed deregistering agent check", "check_id", id, "error", err)
+		// if we couldn't populate remainingChecks it is unlikely that CheckDeregister will work, but try anyway
+		// if we could list the remaining checks, verify that the check we store still exists before removing it.
+		if remainingChecks == nil || checkRemains(id) {
+			if err := c.client.CheckDeregister(id); err != nil {
+				c.logger.Error("failed deregistering agent check", "check_id", id, "error", err)
+			}
 		}
 	}