diff --git a/.changeset/cyan-coins-guess.md b/.changeset/cyan-coins-guess.md
new file mode 100644
index 000000000..9ce87a015
--- /dev/null
+++ b/.changeset/cyan-coins-guess.md
@@ -0,0 +1,5 @@
+---
+'myst-templates': patch
+---
+
+Only add author affiliations/contrib to template doc
diff --git a/.changeset/light-shirts-tease.md b/.changeset/light-shirts-tease.md
new file mode 100644
index 000000000..71d4c255d
--- /dev/null
+++ b/.changeset/light-shirts-tease.md
@@ -0,0 +1,5 @@
+---
+'myst-to-jats': patch
+---
+
+JATS only includes authors as top-level contribs
diff --git a/.changeset/metal-pans-remember.md b/.changeset/metal-pans-remember.md
new file mode 100644
index 000000000..9fc23e0f4
--- /dev/null
+++ b/.changeset/metal-pans-remember.md
@@ -0,0 +1,5 @@
+---
+'myst-to-jats': patch
+---
+
+Remove contrib id, authors cannot be referenced.
diff --git a/.changeset/purple-dancers-report.md b/.changeset/purple-dancers-report.md
new file mode 100644
index 000000000..8506399da
--- /dev/null
+++ b/.changeset/purple-dancers-report.md
@@ -0,0 +1,5 @@
+---
+'myst-to-jats': patch
+---
+
+JATS only includes author affiliations in aff list
diff --git a/packages/myst-templates/src/frontmatter.spec.ts b/packages/myst-templates/src/frontmatter.spec.ts
index 3ed9dfbd3..80dd9eb72 100644
--- a/packages/myst-templates/src/frontmatter.spec.ts
+++ b/packages/myst-templates/src/frontmatter.spec.ts
@@ -164,4 +164,119 @@ describe('extendFrontmatter', () => {
       },
     ]);
   });
+  it('affiliations are only used from authors', async () => {
+    const frontmatter: PageFrontmatter = {
+      authors: [
+        {
+          name: 'John Doe',
+          affiliations: ['aff1'],
+        },
+        {
+          name: 'Jane Doe',
+          affiliations: ['aff1', 'col2'],
+        },
+      ],
+      affiliations: [
+        {
+          id: 'aff1',
+          name: 'univ 1',
+        },
+        {
+          id: 'aff2',
+          name: 'univ 2',
+        },
+        {
+          id: 'col1',
+          name: 'group 1',
+          collaboration: true,
+        },
+        {
+          id: 'col2',
+          name: 'group 2',
+          collaboration: true,
+        },
+      ],
+    };
+    const doc = extendFrontmatter(frontmatter);
+    expect(doc.authors).toEqual([
+      {
+        name: 'John Doe',
+        given_name: 'John',
+        surname: 'Doe',
+        index: 1,
+        letter: 'A',
+        affiliations: [
+          {
+            id: 'aff1',
+            name: 'univ 1',
+            value: {
+              id: 'aff1',
+              name: 'univ 1',
+            },
+            index: 1,
+            letter: 'A',
+          },
+        ],
+      },
+      {
+        name: 'Jane Doe',
+        given_name: 'Jane',
+        surname: 'Doe',
+        index: 2,
+        letter: 'B',
+        affiliations: [
+          {
+            id: 'aff1',
+            name: 'univ 1',
+            value: {
+              id: 'aff1',
+              name: 'univ 1',
+            },
+            index: 1,
+            letter: 'A',
+          },
+        ],
+        collaborations: [
+          {
+            id: 'col2',
+            name: 'group 2',
+            collaboration: true,
+            value: {
+              id: 'col2',
+              name: 'group 2',
+              collaboration: true,
+            },
+            index: 1,
+            letter: 'A',
+          },
+        ],
+      },
+    ]);
+    expect(doc.affiliations).toEqual([
+      {
+        id: 'aff1',
+        name: 'univ 1',
+        value: {
+          id: 'aff1',
+          name: 'univ 1',
+        },
+        index: 1,
+        letter: 'A',
+      },
+    ]);
+    expect(doc.collaborations).toEqual([
+      {
+        id: 'col2',
+        name: 'group 2',
+        collaboration: true,
+        value: {
+          id: 'col2',
+          name: 'group 2',
+          collaboration: true,
+        },
+        index: 1,
+        letter: 'A',
+      },
+    ]);
+  });
 });
diff --git a/packages/myst-templates/src/frontmatter.ts b/packages/myst-templates/src/frontmatter.ts
index fbb9b264d..0cb3eb29d 100644
--- a/packages/myst-templates/src/frontmatter.ts
+++ b/packages/myst-templates/src/frontmatter.ts
@@ -1,4 +1,4 @@
-import type { Contributor, PageFrontmatter } from 'myst-frontmatter';
+import type { Affiliation, Contributor, PageFrontmatter } from 'myst-frontmatter';
 import type { RendererAuthor, RendererDoc, ValueAndIndex } from './types.js';
 
 const ALPHA = 'ABCDEFGHIJKLMNOPQURSUVWXYZ';
@@ -71,18 +71,22 @@ function addIndicesToAuthors(
 
 export function extendFrontmatter(frontmatter: PageFrontmatter): RendererDoc {
   const datetime = frontmatter.date ? new Date(frontmatter.date) : new Date();
-  const affiliations =
-    frontmatter.affiliations
-      ?.filter((aff) => aff.id && !aff.collaboration)
-      .map((aff, index) => {
-        return { ...aff, value: aff, ...indexAndLetter(index) };
-      }) ?? [];
-  const collaborations =
-    frontmatter.affiliations
-      ?.filter((aff) => aff.id && aff.collaboration)
-      .map((aff, index) => {
-        return { ...aff, value: aff, ...indexAndLetter(index) };
-      }) ?? [];
+  // Only add affiliations from authors, not contributors
+  const affIds = [
+    ...new Set(frontmatter.authors?.map((auth) => auth.affiliations ?? []).flat() ?? []),
+  ];
+  const affiliations = affIds
+    .map((id) => frontmatter.affiliations?.find((aff) => aff.id === id))
+    .filter((aff): aff is Affiliation => !!aff?.id && !aff.collaboration)
+    .map((aff, index) => {
+      return { ...aff, value: aff, ...indexAndLetter(index) };
+    });
+  const collaborations = affIds
+    .map((id) => frontmatter.affiliations?.find((aff) => aff.id === id))
+    .filter((aff): aff is Affiliation => !!aff?.id && !!aff.collaboration)
+    .map((aff, index) => {
+      return { ...aff, value: aff, ...indexAndLetter(index) };
+    });
   const doc: RendererDoc = {
     ...frontmatter,
     date: {
diff --git a/packages/myst-to-jats/src/frontmatter.ts b/packages/myst-to-jats/src/frontmatter.ts
index 9cf9730b9..805e215a9 100644
--- a/packages/myst-to-jats/src/frontmatter.ts
+++ b/packages/myst-to-jats/src/frontmatter.ts
@@ -160,7 +160,6 @@ export function getArticleAuthors(frontmatter: ProjectFrontmatter): Element[] {
     const attributes: Record<string, any> = {};
     const elements: Element[] = [];
     if (type) attributes['contrib-type'] = type;
-    if (author.id) attributes.id = author.id;
     if (author.corresponding) attributes.corresp = 'yes';
     if (author.deceased) attributes['deceased'] = 'yes';
     if (author.equal_contributor != null) {
@@ -228,16 +227,10 @@ export function getArticleAuthors(frontmatter: ProjectFrontmatter): Element[] {
   const authorContribs = (frontmatter.authors ?? []).map((author): Element => {
     return generateContrib(author, 'author');
   });
-  const otherContribs = (frontmatter.contributors ?? []).map((contributor): Element => {
-    return generateContrib(contributor);
-  });
   const contribGroups: Element[] = [];
   if (authorContribs.length) {
     contribGroups.push({ type: 'element', name: 'contrib-group', elements: authorContribs });
   }
-  if (otherContribs.length) {
-    contribGroups.push({ type: 'element', name: 'contrib-group', elements: otherContribs });
-  }
   return contribGroups;
 }
 
@@ -309,84 +302,93 @@ function instWrapElementsFromAffiliation(affiliation: Affiliation, includeDept =
 }
 
 export function getArticleAffiliations(frontmatter: ProjectFrontmatter): Element[] {
-  const affs = frontmatter.affiliations?.map((affiliation): Element => {
-    const elements: Element[] = [];
-    const attributes: Record<string, any> = {};
-    if (affiliation.id) {
-      attributes.id = affiliation.id;
-    }
-    elements.push(...instWrapElementsFromAffiliation(affiliation));
-    if (affiliation.address) {
-      elements.push({
-        type: 'element',
-        name: 'addr-line',
-        elements: [{ type: 'text', text: affiliation.address }],
-      });
-    }
-    if (affiliation.city) {
-      elements.push({
-        type: 'element',
-        name: 'city',
-        elements: [{ type: 'text', text: affiliation.city }],
-      });
-    }
-    if (affiliation.state) {
-      elements.push({
-        type: 'element',
-        name: 'state',
-        elements: [{ type: 'text', text: affiliation.state }],
-      });
-    }
-    if (affiliation.postal_code) {
-      elements.push({
-        type: 'element',
-        name: 'postal-code',
-        elements: [{ type: 'text', text: affiliation.postal_code }],
-      });
-    }
-    if (affiliation.country) {
-      elements.push({
-        type: 'element',
-        name: 'country',
-        elements: [{ type: 'text', text: affiliation.country }],
-      });
-    }
-    if (affiliation.phone) {
-      elements.push({
-        type: 'element',
-        name: 'phone',
-        elements: [{ type: 'text', text: affiliation.phone }],
-      });
-    }
-    if (affiliation.fax) {
-      elements.push({
-        type: 'element',
-        name: 'fax',
-        elements: [{ type: 'text', text: affiliation.fax }],
-      });
-    }
-    if (affiliation.email) {
-      elements.push({
-        type: 'element',
-        name: 'email',
-        elements: [{ type: 'text', text: affiliation.email }],
-      });
-    }
-    if (affiliation.url) {
-      elements.push({
+  if (!frontmatter.affiliations?.length) return [];
+  // Only add affiliations from authors, not contributors
+  const affIds = [
+    ...new Set(frontmatter.authors?.map((auth) => auth.affiliations ?? []).flat() ?? []),
+  ];
+  if (!affIds?.length) return [];
+  const affs = affIds
+    .map((id) => frontmatter.affiliations?.find((aff) => aff.id === id))
+    .filter((aff): aff is Affiliation => !!aff)
+    .map((affiliation): Element => {
+      const elements: Element[] = [];
+      const attributes: Record<string, any> = {};
+      if (affiliation.id) {
+        attributes.id = affiliation.id;
+      }
+      elements.push(...instWrapElementsFromAffiliation(affiliation));
+      if (affiliation.address) {
+        elements.push({
+          type: 'element',
+          name: 'addr-line',
+          elements: [{ type: 'text', text: affiliation.address }],
+        });
+      }
+      if (affiliation.city) {
+        elements.push({
+          type: 'element',
+          name: 'city',
+          elements: [{ type: 'text', text: affiliation.city }],
+        });
+      }
+      if (affiliation.state) {
+        elements.push({
+          type: 'element',
+          name: 'state',
+          elements: [{ type: 'text', text: affiliation.state }],
+        });
+      }
+      if (affiliation.postal_code) {
+        elements.push({
+          type: 'element',
+          name: 'postal-code',
+          elements: [{ type: 'text', text: affiliation.postal_code }],
+        });
+      }
+      if (affiliation.country) {
+        elements.push({
+          type: 'element',
+          name: 'country',
+          elements: [{ type: 'text', text: affiliation.country }],
+        });
+      }
+      if (affiliation.phone) {
+        elements.push({
+          type: 'element',
+          name: 'phone',
+          elements: [{ type: 'text', text: affiliation.phone }],
+        });
+      }
+      if (affiliation.fax) {
+        elements.push({
+          type: 'element',
+          name: 'fax',
+          elements: [{ type: 'text', text: affiliation.fax }],
+        });
+      }
+      if (affiliation.email) {
+        elements.push({
+          type: 'element',
+          name: 'email',
+          elements: [{ type: 'text', text: affiliation.email }],
+        });
+      }
+      if (affiliation.url) {
+        elements.push({
+          type: 'element',
+          name: 'ext-link',
+          attributes: { 'ext-link-type': 'uri', 'xlink:href': affiliation.url },
+          elements: [{ type: 'text', text: affiliation.url }],
+        });
+      }
+      return {
         type: 'element',
-        name: 'ext-link',
-        attributes: { 'ext-link-type': 'uri', 'xlink:href': affiliation.url },
-        elements: [{ type: 'text', text: affiliation.url }],
-      });
-    }
-    return {
-      type: 'element',
-      name: 'aff',
-      attributes,
-      elements,
-    };
-  });
+        name: 'aff',
+        attributes,
+        elements,
+      };
+    });
   return affs ? affs : [];
 }
 
diff --git a/packages/myst-to-jats/tests/affiliations.yml b/packages/myst-to-jats/tests/affiliations.yml
index 116fe8f1d..6efacbce0 100644
--- a/packages/myst-to-jats/tests/affiliations.yml
+++ b/packages/myst-to-jats/tests/affiliations.yml
@@ -8,6 +8,11 @@ cases:
             - type: text
               value: text
     frontmatter:
+      authors:
+        - name: John Doe
+          affiliations:
+            - univa
+            - univb
       affiliations:
         - id: univa
           name: University A
@@ -32,6 +37,16 @@ cases:
       <article xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:ali="http://www.niso.org/schemas/ali/1.0/" dtd-version="1.3" xml:lang="en">
         <front>
           <article-meta>
+            <contrib-group>
+              <contrib contrib-type="author">
+                <name name-style="western">
+                  <surname>Doe</surname>
+                  <given-names>John</given-names>
+                </name>
+                <xref ref-type="aff" rid="univa"/>
+                <xref ref-type="aff" rid="univb"/>
+              </contrib>
+            </contrib-group>
             <aff id="univa">
               <institution-wrap>
                 <institution>University A</institution>
diff --git a/packages/myst-to-jats/tests/authors.yml b/packages/myst-to-jats/tests/authors.yml
index 844e41b42..37d3c5565 100644
--- a/packages/myst-to-jats/tests/authors.yml
+++ b/packages/myst-to-jats/tests/authors.yml
@@ -44,7 +44,7 @@ cases:
         <front>
           <article-meta>
             <contrib-group>
-              <contrib contrib-type="author" id="contributors-generated-uid-0" corresp="yes" deceased="yes" equal-contrib="no">
+              <contrib contrib-type="author" corresp="yes" deceased="yes" equal-contrib="no">
                 <contrib-id contrib-id-type="orcid">0000-0000-0000-0000</contrib-id>
                 <name name-style="western">
                   <surname>Doe</surname>
@@ -58,14 +58,14 @@ cases:
                 <email>example@example.com</email>
                 <ext-link ext-link-type="uri" xlink:href="https://example.com">https://example.com</ext-link>
               </contrib>
-              <contrib contrib-type="author" id="contributors-generated-uid-1">
+              <contrib contrib-type="author">
                 <name name-style="western">
                   <surname>Doe</surname>
                   <given-names>John</given-names>
                   <suffix>Jr.</suffix>
                 </name>
               </contrib>
-              <contrib contrib-type="author" id="contributors-generated-uid-2">
+              <contrib contrib-type="author">
                 <string-name name-style="western">John Doe III</string-name>
               </contrib>
             </contrib-group>
diff --git a/packages/myst-to-jats/tests/funding.yml b/packages/myst-to-jats/tests/funding.yml
index 9d8a04958..964205b37 100644
--- a/packages/myst-to-jats/tests/funding.yml
+++ b/packages/myst-to-jats/tests/funding.yml
@@ -79,26 +79,13 @@ cases:
         <front>
           <article-meta>
             <contrib-group>
-              <contrib contrib-type="author" id="John Doe">
+              <contrib contrib-type="author">
                 <name name-style="western">
                   <surname>Doe</surname>
                   <given-names>John</given-names>
                 </name>
               </contrib>
             </contrib-group>
-            <contrib-group>
-              <contrib id="Jane Doe">
-                <name name-style="western">
-                  <surname>Doe</surname>
-                  <given-names>Jane</given-names>
-                </name>
-              </contrib>
-            </contrib-group>
-            <aff id="University A">
-              <institution-wrap>
-                <institution>University A</institution>
-              </institution-wrap>
-            </aff>
             <funding-group>
               <award-group>
                 <funding-source>
@@ -181,7 +168,7 @@ cases:
         <front>
           <article-meta>
             <contrib-group>
-              <contrib contrib-type="author" id="jd">
+              <contrib contrib-type="author">
                 <contrib-id contrib-id-type="orcid">0000-0000-0000-0000</contrib-id>
                 <name name-style="western">
                   <surname>Doe</surname>
@@ -190,19 +177,6 @@ cases:
                 <xref ref-type="aff" rid="univa"/>
               </contrib>
             </contrib-group>
-            <contrib-group>
-              <contrib id="contributors-generated-uid-1">
-                <name name-style="western">
-                  <surname>Doe</surname>
-                  <given-names>Jane</given-names>
-                </name>
-              </contrib>
-            </contrib-group>
-            <aff id="univb">
-              <institution-wrap>
-                <institution>University B</institution>
-              </institution-wrap>
-            </aff>
             <aff id="univa">
               <institution-wrap>
                 <institution>University A</institution>
@@ -211,11 +185,6 @@ cases:
                 <institution content-type="dept">Some Department</institution>
               </institution-wrap>
             </aff>
-            <aff id="University C">
-              <institution-wrap>
-                <institution>University C</institution>
-              </institution-wrap>
-            </aff>
             <funding-group>
               <award-group>
                 <funding-source>
@@ -327,7 +296,7 @@ cases:
         <front>
           <article-meta>
             <contrib-group>
-              <contrib contrib-type="author" id="jd">
+              <contrib contrib-type="author">
                 <contrib-id contrib-id-type="orcid">0000-0000-0000-0000</contrib-id>
                 <name name-style="western">
                   <surname>Doe</surname>
@@ -336,15 +305,6 @@ cases:
                 <xref ref-type="aff" rid="univa"/>
               </contrib>
             </contrib-group>
-            <aff id="univb">
-              <institution-wrap>
-                <institution>University B</institution>
-                <institution-id institution-id-type="isni">0000000000000001</institution-id>
-                <institution-id institution-id-type="ringgold">99998</institution-id>
-                <institution-id institution-id-type="ror">0000000000000001</institution-id>
-                <institution-id institution-id-type="doi">10.1000/efg012</institution-id>
-              </institution-wrap>
-            </aff>
             <aff id="univa">
               <institution-wrap>
                 <institution>University A</institution>
diff --git a/packages/myst-to-jats/tests/multi.yml b/packages/myst-to-jats/tests/multi.yml
index 0cdaf03a2..d2b2e276d 100644
--- a/packages/myst-to-jats/tests/multi.yml
+++ b/packages/myst-to-jats/tests/multi.yml
@@ -167,21 +167,13 @@ cases:
               <article-title>Top title</article-title>
             </title-group>
             <contrib-group>
-              <contrib contrib-type="author" id="Author One">
+              <contrib contrib-type="author">
                 <name name-style="western">
                   <surname>One</surname>
                   <given-names>Author</given-names>
                 </name>
               </contrib>
             </contrib-group>
-            <contrib-group>
-              <contrib id="Author Two">
-                <name name-style="western">
-                  <surname>Two</surname>
-                  <given-names>Author</given-names>
-                </name>
-              </contrib>
-            </contrib-group>
             <funding-group>
               <award-group>
                 <principal-investigator>
@@ -200,7 +192,7 @@ cases:
         <sub-article>
           <front-stub>
             <contrib-group>
-              <contrib contrib-type="author" id="Author Three">
+              <contrib contrib-type="author">
                 <name name-style="western">
                   <surname>Three</surname>
                   <given-names>Author</given-names>