diff --git a/CHANGELOG.md b/CHANGELOG.md
index 97d7a41d..2677a163 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -11,6 +11,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### `Fixed`
 
+- [#800](https://github.com/nf-core/ampliseq/pull/800) - Fixed SH files for UNITE9.0, they were missing some entries due to a bug caused by API update in PlutoF
+
 ### `Dependencies`
 
 - [#797](https://github.com/nf-core/ampliseq/pull/797) - Update QIIME2
diff --git a/conf/ref_databases.config b/conf/ref_databases.config
index ef03bdcb..876e0dac 100644
--- a/conf/ref_databases.config
+++ b/conf/ref_databases.config
@@ -204,7 +204,7 @@ params {
             citation = "Abarenkov, Kessy; Zirk, Allan; Piirmann, Timo; Pöhönen, Raivo; Ivanov, Filipp; Nilsson, R. Henrik; Kõljalg, Urmas (2023): UNITE general FASTA release for Fungi. Version 18.07.2023. UNITE Community. https://doi.org/10.15156/BIO/2938067"
             fmtscript = "taxref_reformat_unite.sh"
             dbversion = "UNITE-fungi v9.0 (https://doi.org/10.15156/BIO/2938067)"
-            shfile = [ "https://figshare.scilifelab.se/ndownloader/files/40788767", "https://figshare.scilifelab.se/ndownloader/files/40788770"]
+            shfile = [ "https://figshare.scilifelab.se/ndownloader/files/50055762", "https://figshare.scilifelab.se/ndownloader/files/50055765"]
         }
         'unite-fungi=9.0' {
             title = "UNITE general FASTA release for Fungi - Version 9.0"
@@ -212,7 +212,7 @@ params {
             citation = "Abarenkov, Kessy; Zirk, Allan; Piirmann, Timo; Pöhönen, Raivo; Ivanov, Filipp; Nilsson, R. Henrik; Kõljalg, Urmas (2023): UNITE general FASTA release for Fungi. Version 18.07.2023. UNITE Community. https://doi.org/10.15156/BIO/2938067"
             fmtscript = "taxref_reformat_unite.sh"
             dbversion = "UNITE-fungi v9.0 (https://doi.org/10.15156/BIO/2938067)"
-            shfile = [ "https://figshare.scilifelab.se/ndownloader/files/40788767", "https://figshare.scilifelab.se/ndownloader/files/40788770"]
+            shfile = [ "https://figshare.scilifelab.se/ndownloader/files/50055762", "https://figshare.scilifelab.se/ndownloader/files/50055765"]
         }
         'unite-fungi=8.3' {
             title = "UNITE general FASTA release for Fungi - Version 8.3"
@@ -236,7 +236,7 @@ params {
             citation = "Abarenkov, Kessy; Zirk, Allan; Piirmann, Timo; Pöhönen, Raivo; Ivanov, Filipp; Nilsson, R. Henrik; Kõljalg, Urmas (2023): UNITE general FASTA release for eukaryotes. Version 18.07.2023. UNITE Community. https://doi.org/10.15156/BIO/2938069"
             fmtscript = "taxref_reformat_unite.sh"
             dbversion = "UNITE-alleuk v9.0 (https://doi.org/10.15156/BIO/2938069)"
-            shfile = [ "https://figshare.scilifelab.se/ndownloader/files/40788773", "https://figshare.scilifelab.se/ndownloader/files/40788776"]
+            shfile = [ "https://figshare.scilifelab.se/ndownloader/files/50055768", "https://figshare.scilifelab.se/ndownloader/files/50055771"]
         }
         'unite-alleuk=9.0' {
             title = "UNITE general FASTA release for eukaryotes - Version 9.0"
@@ -244,7 +244,7 @@ params {
             citation = "Abarenkov, Kessy; Zirk, Allan; Piirmann, Timo; Pöhönen, Raivo; Ivanov, Filipp; Nilsson, R. Henrik; Kõljalg, Urmas (2023): UNITE general FASTA release for eukaryotes. Version 18.07.2023. UNITE Community. https://doi.org/10.15156/BIO/2938069"
             fmtscript = "taxref_reformat_unite.sh"
             dbversion = "UNITE-alleuk v9.0 (https://doi.org/10.15156/BIO/2938069)"
-            shfile = [ "https://figshare.scilifelab.se/ndownloader/files/40788773", "https://figshare.scilifelab.se/ndownloader/files/40788776"]
+            shfile = [ "https://figshare.scilifelab.se/ndownloader/files/50055768", "https://figshare.scilifelab.se/ndownloader/files/50055771"]
         }
         'unite-alleuk=8.3' {
             title = "UNITE general FASTA release for eukaryotes - Version 8.3"