diff --git a/modules/auth/auth.go b/modules/auth/auth.go
index 4be358b73..3dca4c2eb 100644
--- a/modules/auth/auth.go
+++ b/modules/auth/auth.go
@@ -214,9 +214,10 @@ func SignedInUser(ctx *macaron.Context, sess session.Store) (*models.User, bool)
 					}
 					return nil, false
 				}
+			} else {
+				ctx.Data["IsApiToken"] = true
 			}
 
-			ctx.Data["IsApiToken"] = true
 			return u, true
 		}
 	}
diff --git a/modules/context/api.go b/modules/context/api.go
index b27ffcbc8..7b49eb8b9 100644
--- a/modules/context/api.go
+++ b/modules/context/api.go
@@ -110,6 +110,28 @@ func (ctx *APIContext) RequireCSRF() {
 	}
 }
 
+// CheckForOTP validateds OTP
+func (ctx *APIContext) CheckForOTP() {
+	otpHeader := ctx.Req.Header.Get("X-Gitea-OTP")
+	twofa, err := models.GetTwoFactorByUID(ctx.Context.User.ID)
+	if err != nil {
+		if models.IsErrTwoFactorNotEnrolled(err) {
+			return // No 2FA enrollment for this user
+		}
+		ctx.Context.Error(500)
+		return
+	}
+	ok, err := twofa.ValidateTOTP(otpHeader)
+	if err != nil {
+		ctx.Context.Error(500)
+		return
+	}
+	if !ok {
+		ctx.Context.Error(401)
+		return
+	}
+}
+
 // APIContexter returns apicontext as macaron middleware
 func APIContexter() macaron.Handler {
 	return func(c *Context) {
diff --git a/modules/context/auth.go b/modules/context/auth.go
index ca897de6e..772403bda 100644
--- a/modules/context/auth.go
+++ b/modules/context/auth.go
@@ -1,10 +1,12 @@
 // Copyright 2014 The Gogs Authors. All rights reserved.
+// Copyright 2019 The Gitea Authors. All rights reserved.
 // Use of this source code is governed by a MIT-style
 // license that can be found in the LICENSE file.
 
 package context
 
 import (
+	"code.gitea.io/gitea/models"
 	"code.gitea.io/gitea/modules/auth"
 	"code.gitea.io/gitea/modules/log"
 	"code.gitea.io/gitea/modules/setting"
@@ -88,6 +90,28 @@ func Toggle(options *ToggleOptions) macaron.Handler {
 				ctx.HTML(200, "user/auth/activate")
 				return
 			}
+			if ctx.IsSigned && auth.IsAPIPath(ctx.Req.URL.Path) && ctx.IsBasicAuth {
+				twofa, err := models.GetTwoFactorByUID(ctx.User.ID)
+				if err != nil {
+					if models.IsErrTwoFactorNotEnrolled(err) {
+						return // No 2FA enrollment for this user
+					}
+					ctx.Error(500)
+					return
+				}
+				otpHeader := ctx.Req.Header.Get("X-Gitea-OTP")
+				ok, err := twofa.ValidateTOTP(otpHeader)
+				if err != nil {
+					ctx.Error(500)
+					return
+				}
+				if !ok {
+					ctx.JSON(403, map[string]string{
+						"message": "Only signed in user is allowed to call APIs.",
+					})
+					return
+				}
+			}
 		}
 
 		// Redirect to log in page if auto-signin info is provided and has not signed in.
diff --git a/routers/api/v1/api.go b/routers/api/v1/api.go
index 89d277233..f377e3090 100644
--- a/routers/api/v1/api.go
+++ b/routers/api/v1/api.go
@@ -172,6 +172,10 @@ func reqToken() macaron.Handler {
 		if true == ctx.Data["IsApiToken"] {
 			return
 		}
+		if ctx.Context.IsBasicAuth {
+			ctx.CheckForOTP()
+			return
+		}
 		if ctx.IsSigned {
 			ctx.RequireCSRF()
 			return
@@ -181,11 +185,12 @@ func reqToken() macaron.Handler {
 }
 
 func reqBasicAuth() macaron.Handler {
-	return func(ctx *context.Context) {
-		if !ctx.IsBasicAuth {
-			ctx.Error(401)
+	return func(ctx *context.APIContext) {
+		if !ctx.Context.IsBasicAuth {
+			ctx.Context.Error(401)
 			return
 		}
+		ctx.CheckForOTP()
 	}
 }