diff --git a/locales/en.json b/locales/en.json
index 637671a2d..efeb66e69 100644
--- a/locales/en.json
+++ b/locales/en.json
@@ -254,5 +254,6 @@
     "certmanager_old_letsencrypt_app_detected" : "\nYunohost detected that the 'letsencrypt' app is installed, which conflits with the new built-in certificate management features in Yunohost. If you wish to use the new built-in features, please run the following commands to migrate your installation :\n\n    yunohost app remove letsencrypt\n    yunohost domain cert-install\n\nN.B. : this will attempt to re-install certificates for all domains with a Let's Encrypt certificate or self-signed certificate.",
     "certmanager_hit_rate_limit" :"Too many certificates already issued for exact set of domains {domain:s} recently. Please try again later. See https://letsencrypt.org/docs/rate-limits/ for more details.",
     "certmanager_cert_signing_failed" : "Signing the new certificate failed.",
-    "certmanager_no_cert_file" : "Unable to read certificate file for domain {domain:s} (file : {file:s})"
+    "certmanager_no_cert_file" : "Unable to read certificate file for domain {domain:s} (file : {file:s})",
+    "certmanager_conflicting_nginx_file": "Unable to prepare domain for ACME challenge : the nginx configuration file {filepath:s} is conflicting and should be removed first."
 }
diff --git a/src/yunohost/certificate.py b/src/yunohost/certificate.py
index d892e6f21..d9110b79b 100644
--- a/src/yunohost/certificate.py
+++ b/src/yunohost/certificate.py
@@ -32,6 +32,7 @@ import smtplib
 import requests
 import subprocess
 import dns.resolver
+import glob
 
 from OpenSSL import crypto
 from datetime import datetime
@@ -152,15 +153,9 @@ def certificate_install(auth, domain_list, force=False, no_checks=False, self_si
 
 
 def _certificate_install_selfsigned(domain_list, force=False):
+
     for domain in domain_list:
 
-        # Check we ain't trying to overwrite a good cert !
-        if (not force) :
-            status = _get_status(domain)
-
-            if status["summary"]["code"] in ('good', 'great') :
-                raise MoulinetteError(errno.EINVAL, m18n.n('certmanager_attempt_to_replace_valid_cert', domain=domain))
-
         # Paths of files and folder we'll need
         date_tag = datetime.now().strftime("%Y%m%d.%H%M%S")
         new_cert_folder = "%s/%s-history/%s-selfsigned" % (CERT_FOLDER, domain, date_tag)
@@ -175,6 +170,14 @@ def _certificate_install_selfsigned(domain_list, force=False):
         crt_file = os.path.join(new_cert_folder, "crt.pem")
         ca_file = os.path.join(new_cert_folder, "ca.pem")
 
+        # Check we ain't trying to overwrite a good cert !
+        current_cert_file = os.path.join(CERT_FOLDER, domain, "crt.pem")
+        if (not force) and (os.path.isfile(current_cert_file)):
+            status = _get_status(domain)
+
+            if status["summary"]["code"] in ('good', 'great') :
+                raise MoulinetteError(errno.EINVAL, m18n.n('certmanager_attempt_to_replace_valid_cert', domain=domain))
+
         # Create output folder for new certificate stuff
         os.makedirs(new_cert_folder)
 
@@ -261,7 +264,7 @@ def _certificate_install_letsencrypt(auth, domain_list, force=False, no_checks=F
 
     if (staging):
         logger.warning("Please note that you used the --staging option, and that no new certificate will actually be enabled !")
-    
+
     # Actual install steps
     for domain in domain_list:
 
@@ -336,7 +339,7 @@ def certificate_renew(auth, domain_list, force=False, no_checks=False, email=Fal
 
     if (staging):
         logger.warning("Please note that you used the --staging option, and that no new certificate will actually be enabled !")
-    
+
     # Actual renew steps
     for domain in domain_list:
         logger.info("Now attempting renewing of certificate for domain %s !", domain)
@@ -421,7 +424,9 @@ Subject: %s
 
 
 def _configure_for_acme_challenge(auth, domain):
-    nginx_conf_file = "/etc/nginx/conf.d/%s.d/000-acmechallenge.conf" % domain
+
+    nginx_conf_folder = "/etc/nginx/conf.d/%s.d" % domain
+    nginx_conf_file = "%s/000-acmechallenge.conf" % nginx_conf_folder
 
     nginx_configuration = '''
 location '/.well-known/acme-challenge'
@@ -431,6 +436,15 @@ location '/.well-known/acme-challenge'
 }
     ''' % WEBROOT_FOLDER
 
+    # Check there isn't a conflicting file for the acme-challenge well-known uri
+    for path in glob.glob('%s/*.conf' % nginx_conf_folder):
+        if (path == nginx_conf_file) :
+            continue
+        with open(path) as f:
+            contents = f.read()
+        if ('/.well-known/acme-challenge' in contents) :
+            raise MoulinetteError(errno.EINVAL, m18n.n('certmanager_conflicting_nginx_file', filepath=path))
+
     # Write the conf
     if os.path.exists(nginx_conf_file):
         logger.info("Nginx configuration file for ACME challenge already exists for domain, skipping.")
@@ -564,6 +578,7 @@ def _prepare_certificate_signing_request(domain, key_file, output_folder):
 
 
 def _get_status(domain):
+
     cert_file = os.path.join(CERT_FOLDER, domain, "crt.pem")
 
     if not os.path.isfile(cert_file):