diff --git a/agent/config/builder.go b/agent/config/builder.go
index d2fa6a888f..a98ab39585 100644
--- a/agent/config/builder.go
+++ b/agent/config/builder.go
@@ -232,6 +232,19 @@ func (b *Builder) Build() (rt RuntimeConfig, err error) {
 		if err != nil {
 			return RuntimeConfig{}, fmt.Errorf("Error parsing %s: %s", s.Name, err)
 		}
+
+		// if we have a single 'check' or 'service' we need to add them to the
+		// list of checks and services first since we cannot merge them
+		// generically and later values would clobber earlier ones.
+		if c2.Check != nil {
+			c2.Checks = append(c2.Checks, *c2.Check)
+			c2.Check = nil
+		}
+		if c2.Service != nil {
+			c2.Services = append(c2.Services, *c2.Service)
+			c2.Service = nil
+		}
+
 		c = Merge(c, c2)
 	}
 
diff --git a/agent/config/runtime_test.go b/agent/config/runtime_test.go
index 4d81de850b..29c3fb1f1e 100644
--- a/agent/config/runtime_test.go
+++ b/agent/config/runtime_test.go
@@ -1657,6 +1657,48 @@ func TestConfigFlagsAndEdgecases(t *testing.T) {
 			},
 			warns: []string{`WARNING: WAN keyring exists but -encrypt given, using keyring`},
 		},
+		{
+			desc: "multiple check files",
+			flags: []string{
+				`-data-dir=` + dataDir,
+			},
+			json: []string{
+				`{ "check": { "name": "a", "script": "/bin/true" } }`,
+				`{ "check": { "name": "b", "script": "/bin/false" } }`,
+			},
+			hcl: []string{
+				`check = { name = "a" script = "/bin/true" }`,
+				`check = { name = "b" script = "/bin/false" }`,
+			},
+			patch: func(rt *RuntimeConfig) {
+				rt.Checks = []*structs.CheckDefinition{
+					&structs.CheckDefinition{Name: "a", Script: "/bin/true"},
+					&structs.CheckDefinition{Name: "b", Script: "/bin/false"},
+				}
+				rt.DataDir = dataDir
+			},
+		},
+		{
+			desc: "multiple service files",
+			flags: []string{
+				`-data-dir=` + dataDir,
+			},
+			json: []string{
+				`{ "service": { "name": "a", "port": 80 } }`,
+				`{ "service": { "name": "b", "port": 90 } }`,
+			},
+			hcl: []string{
+				`service = { name = "a" port = 80 }`,
+				`service = { name = "b" port = 90 }`,
+			},
+			patch: func(rt *RuntimeConfig) {
+				rt.Services = []*structs.ServiceDefinition{
+					&structs.ServiceDefinition{Name: "a", Port: 80},
+					&structs.ServiceDefinition{Name: "b", Port: 90},
+				}
+				rt.DataDir = dataDir
+			},
+		},
 	}
 
 	testConfig(t, tests, dataDir)
@@ -2831,29 +2873,6 @@ func TestFullConfig(t *testing.T) {
 		CAPath:                           "mQEN1Mfp",
 		CertFile:                         "7s4QAzDk",
 		Checks: []*structs.CheckDefinition{
-			&structs.CheckDefinition{
-				ID:        "fZaCAXww",
-				Name:      "OOM2eo0f",
-				Notes:     "zXzXI9Gt",
-				ServiceID: "L8G0QNmR",
-				Token:     "oo4BCTgJ",
-				Status:    "qLykAl5u",
-				Script:    "dhGfIF8n",
-				HTTP:      "29B93haH",
-				Header: map[string][]string{
-					"hBq0zn1q": {"2a9o9ZKP", "vKwA5lR6"},
-					"f3r6xFtM": {"RyuIdDWv", "QbxEcIUM"},
-				},
-				Method:            "Dou0nGT5",
-				TCP:               "JY6fTTcw",
-				Interval:          18714 * time.Second,
-				DockerContainerID: "qF66POS9",
-				Shell:             "sOnDy228",
-				TLSSkipVerify:     true,
-				Timeout:           5954 * time.Second,
-				TTL:               30044 * time.Second,
-				DeregisterCriticalServiceAfter: 13209 * time.Second,
-			},
 			&structs.CheckDefinition{
 				ID:        "uAjE6m9Z",
 				Name:      "QsZRGpYr",
@@ -2900,6 +2919,29 @@ func TestFullConfig(t *testing.T) {
 				TTL:               31006 * time.Second,
 				DeregisterCriticalServiceAfter: 2366 * time.Second,
 			},
+			&structs.CheckDefinition{
+				ID:        "fZaCAXww",
+				Name:      "OOM2eo0f",
+				Notes:     "zXzXI9Gt",
+				ServiceID: "L8G0QNmR",
+				Token:     "oo4BCTgJ",
+				Status:    "qLykAl5u",
+				Script:    "dhGfIF8n",
+				HTTP:      "29B93haH",
+				Header: map[string][]string{
+					"hBq0zn1q": {"2a9o9ZKP", "vKwA5lR6"},
+					"f3r6xFtM": {"RyuIdDWv", "QbxEcIUM"},
+				},
+				Method:            "Dou0nGT5",
+				TCP:               "JY6fTTcw",
+				Interval:          18714 * time.Second,
+				DockerContainerID: "qF66POS9",
+				Shell:             "sOnDy228",
+				TLSSkipVerify:     true,
+				Timeout:           5954 * time.Second,
+				TTL:               30044 * time.Second,
+				DeregisterCriticalServiceAfter: 13209 * time.Second,
+			},
 		},
 		CheckUpdateInterval:       16507 * time.Second,
 		ClientAddrs:               []*net.IPAddr{ipAddr("93.83.18.19")},