diff --git a/.changeset/rotten-timers-worry.md b/.changeset/rotten-timers-worry.md
new file mode 100644
index 000000000..0d50492e5
--- /dev/null
+++ b/.changeset/rotten-timers-worry.md
@@ -0,0 +1,6 @@
+---
+'myst-transforms': patch
+'myst-cli': patch
+---
+
+Improve HTML transforms for grouping and processing
diff --git a/packages/myst-cli/src/process/mdast.ts b/packages/myst-cli/src/process/mdast.ts
index 933f57f2c..f60a512b4 100644
--- a/packages/myst-cli/src/process/mdast.ts
+++ b/packages/myst-cli/src/process/mdast.ts
@@ -24,6 +24,7 @@ import {
   joinGatesPlugin,
   glossaryPlugin,
   abbreviationPlugin,
+  reconstructHtmlPlugin,
 } from 'myst-transforms';
 import { unified } from 'unified';
 import { VFile } from 'vfile';
@@ -164,9 +165,10 @@ export async function transformMdast(
   liftCodeMetadataToBlock(session, vfile, mdast);
 
   const pipe = unified()
+    .use(reconstructHtmlPlugin) // We need to group and link the HTML first
+    .use(htmlPlugin, { htmlHandlers }) // Some of the HTML plugins need to operate on the transformed html, e.g. figure caption transforms
     .use(basicTransformationsPlugin)
     .use(inlineExpressionsPlugin) // Happens before math and images!
-    .use(htmlPlugin, { htmlHandlers })
     .use(mathPlugin, { macros: frontmatter.math })
     .use(glossaryPlugin, { state }) // This should be before the enumerate plugins
     .use(abbreviationPlugin, { abbreviations: frontmatter.abbreviations })
diff --git a/packages/myst-transforms/src/html.spec.ts b/packages/myst-transforms/src/html.spec.ts
index 25ece935f..20f52e366 100644
--- a/packages/myst-transforms/src/html.spec.ts
+++ b/packages/myst-transforms/src/html.spec.ts
@@ -1,5 +1,5 @@
 import { describe, expect, test } from 'vitest';
-import { reconstructHtmlTransform } from './html';
+import { htmlTransform, reconstructHtmlTransform } from './html';
 
 describe('Test reconstructHtmlTransform', () => {
   test('tree without html returns self', async () => {
@@ -162,4 +162,178 @@ describe('Test reconstructHtmlTransform', () => {
       children: [{ type: 'html', value: '<script>alert("error")</script>' }],
     });
   });
+  test('self-closing tags', async () => {
+    const mdast = {
+      type: 'root',
+      children: [
+        {
+          type: 'html',
+          value: '<a href="https://mystmd.org">',
+        },
+        {
+          type: 'html',
+          value: '<img src="https://mystmd.org/logo.png"    />',
+        },
+        {
+          type: 'html',
+          value: '<hr>',
+        },
+        {
+          type: 'html',
+          value: '<br>',
+        },
+        { type: 'html', value: '</a>' },
+      ],
+    };
+    reconstructHtmlTransform(mdast);
+    expect(mdast).toEqual({
+      type: 'root',
+      children: [
+        {
+          type: 'html',
+          value:
+            '<a href="https://mystmd.org"><img src="https://mystmd.org/logo.png">\n<hr>\n<br></a>',
+        },
+      ],
+    });
+  });
+  test('figure captions', async () => {
+    const mdast = {
+      type: 'root',
+      children: [
+        {
+          type: 'html',
+          value: '<figure>',
+        },
+        {
+          type: 'html',
+          value: '<img src="img.png" class="big" id="my-img">',
+        },
+        {
+          type: 'html',
+          value: '<figcaption>',
+        },
+        {
+          type: 'text',
+          value: 'my caption',
+        },
+        {
+          type: 'html',
+          value: '</figcaption>',
+        },
+        {
+          type: 'html',
+          value: '</figure>',
+        },
+      ],
+    };
+    reconstructHtmlTransform(mdast);
+    expect(mdast).toEqual({
+      type: 'root',
+      children: [
+        {
+          type: 'html',
+          value:
+            '<figure><img src="img.png" class="big" id="my-img">\n<figcaption>my caption</figcaption></figure>',
+        },
+      ],
+    });
+    htmlTransform(mdast);
+    expect(mdast).toEqual({
+      type: 'root',
+      children: [
+        {
+          type: 'container',
+          children: [
+            { type: 'image', url: 'img.png', class: 'big', identifier: 'my-img', label: 'my-img' },
+            { type: 'caption', children: [{ type: 'text', value: 'my caption' }] },
+          ],
+        },
+      ],
+    });
+  });
+  test('no paragraph when in a paragraph', async () => {
+    const mdast = {
+      type: 'root',
+      children: [
+        {
+          type: 'paragraph',
+          children: [
+            {
+              type: 'text',
+              value: 'See ',
+            },
+            {
+              type: 'html',
+              value: '<a href="link.html">',
+            },
+            {
+              type: 'text',
+              value: 'here',
+            },
+            {
+              type: 'html',
+              value: '</a>',
+            },
+            {
+              type: 'text',
+              value: '.',
+            },
+          ],
+        },
+      ],
+    };
+    reconstructHtmlTransform(mdast);
+    expect(mdast).toEqual({
+      type: 'root',
+      children: [
+        {
+          type: 'paragraph',
+          children: [
+            {
+              type: 'text',
+              value: 'See ',
+            },
+            {
+              type: 'html',
+              value: '<a href="link.html">here</a>',
+            },
+            {
+              type: 'text',
+              value: '.',
+            },
+          ],
+        },
+      ],
+    });
+    htmlTransform(mdast);
+    expect(mdast).toEqual({
+      type: 'root',
+      children: [
+        {
+          type: 'paragraph',
+          children: [
+            {
+              type: 'text',
+              value: 'See ',
+            },
+            {
+              type: 'link',
+              url: 'link.html',
+              children: [
+                {
+                  type: 'text',
+                  value: 'here',
+                },
+              ],
+            },
+            {
+              type: 'text',
+              value: '.',
+            },
+          ],
+        },
+      ],
+    });
+  });
 });
diff --git a/packages/myst-transforms/src/html.ts b/packages/myst-transforms/src/html.ts
index f3093d018..fe35655e8 100644
--- a/packages/myst-transforms/src/html.ts
+++ b/packages/myst-transforms/src/html.ts
@@ -1,6 +1,6 @@
 import { unified } from 'unified';
 import type { Plugin } from 'unified';
-import { liftChildren } from 'myst-common';
+import { liftChildren, normalizeLabel } from 'myst-common';
 import type { GenericNode, GenericParent } from 'myst-common';
 import type { Parent } from 'myst-spec';
 import { mystToHtml } from 'myst-to-html';
@@ -20,6 +20,17 @@ export type HtmlTransformOptions = {
   htmlHandlers?: { [x: string]: Handle };
 };
 
+function addClassAndIdentifier(node: GenericNode, attrs: Record<string, string> = {}) {
+  const props = node.properties ?? {};
+  if (props.id) {
+    const normalized = normalizeLabel(props.id);
+    if (normalized?.identifier) attrs.identifier = normalized.identifier;
+    if (normalized?.label) attrs.label = normalized.label;
+  }
+  if (props.className) attrs.class = props.className.join(' ');
+  return attrs;
+}
+
 const defaultHtmlToMdastOptions: Record<keyof HtmlTransformOptions, any> = {
   keepBreaks: true,
   htmlHandlers: {
@@ -34,6 +45,27 @@ const defaultHtmlToMdastOptions: Record<keyof HtmlTransformOptions, any> = {
     _brKeep(h: H, node: any) {
       return h(node, '_break');
     },
+    a(h: H, node: any) {
+      const attrs = addClassAndIdentifier(node);
+      attrs.url = String(node.properties.href || '');
+      if (node.properties.title) attrs.title = node.properties.title;
+      if (node.properties.className) attrs.class = node.properties.className.join(' ');
+      return h(node, 'link', attrs, all(h, node));
+    },
+    img(h: H, node: any) {
+      const attrs = addClassAndIdentifier(node);
+      attrs.url = String(node.properties.src || '');
+      if (node.properties.title) attrs.title = node.properties.title;
+      if (node.properties.alt) attrs.alt = node.properties.alt;
+      return h(node, 'image', attrs);
+    },
+    figure(h: H, node: any) {
+      const attrs = addClassAndIdentifier(node);
+      return h(node, 'container', attrs, all(h, node));
+    },
+    figcaption(h: H, node: any) {
+      return h(node, 'caption', all(h, node));
+    },
     comment(h: any, node: any) {
       // Prevents HTML comments from showing up as text in web
       const result = h(node, 'comment');
@@ -66,6 +98,12 @@ export function htmlTransform(tree: GenericParent, opts?: HtmlTransformOptions)
     node.children = mdast.children as Parent[];
     visit(node, (n: any) => delete n.position);
   });
+  selectAll('paragraph > htmlParsed', tree).forEach((parsed) => {
+    const node = parsed as GenericParent;
+    if (node?.children?.length === 1 && node.children[0].type === 'paragraph') {
+      node.children = node.children[0].children as GenericNode[];
+    }
+  });
   liftChildren(tree, 'htmlParsed');
   selectAll('_break', tree).forEach((node: any) => {
     node.type = 'break';
@@ -103,17 +141,41 @@ function finalizeNode(htmlOpenNodeWithChildren: GenericParent, htmlCloseNode: Ge
   delete (htmlOpenNodeWithChildren as GenericNode).children;
 }
 
+// https://html.spec.whatwg.org/multipage/syntax.html#elements-2
+const HTML_EMPTY_ELEMENTS = [
+  'area',
+  'base',
+  'br',
+  'col',
+  'embed',
+  'hr',
+  'img',
+  'input',
+  'keygen',
+  'link',
+  'meta',
+  'param',
+  'source',
+  'track',
+  'wbr',
+];
+
 function reconstructHtml(tree: GenericParent) {
   const htmlOpenNodes: GenericParent[] = [];
   tree.children.forEach((child: GenericNode) => {
     if (child.type === 'html') {
       const value = child.value?.trim();
-      if (value?.startsWith('</')) {
+      const selfClosing =
+        (value?.startsWith('<') && value?.endsWith('/>')) ||
+        value?.match(new RegExp(`<(${HTML_EMPTY_ELEMENTS.join('|')})([^>]*)?/?>`));
+      if (selfClosing) {
+        if (htmlOpenNodes.length) {
+          htmlOpenNodes[htmlOpenNodes.length - 1].children.push(child);
+        }
+      } else if (value?.startsWith('</')) {
         // In this case, child is a standalone closing html node
         const htmlOpenNode = htmlOpenNodes.pop();
-        if (!htmlOpenNode) {
-          return;
-        }
+        if (!htmlOpenNode) return;
         finalizeNode(htmlOpenNode, child);
         if (htmlOpenNodes.length) {
           htmlOpenNodes[htmlOpenNodes.length - 1].children.push(htmlOpenNode);
@@ -152,6 +214,10 @@ export function reconstructHtmlTransform(tree: GenericParent) {
   return tree;
 }
 
+export const reconstructHtmlPlugin: Plugin<[], GenericParent, GenericParent> = () => (tree) => {
+  reconstructHtmlTransform(tree);
+};
+
 export const htmlPlugin: Plugin<[HtmlTransformOptions?], GenericParent, GenericParent> =
   (opts) => (tree) => {
     htmlTransform(tree, opts);
diff --git a/packages/myst-transforms/src/index.ts b/packages/myst-transforms/src/index.ts
index 212b397ad..a388926e8 100644
--- a/packages/myst-transforms/src/index.ts
+++ b/packages/myst-transforms/src/index.ts
@@ -6,7 +6,12 @@ export {
 } from './admonitions.js';
 export { captionParagraphPlugin, captionParagraphTransform } from './caption.js';
 export { footnotesPlugin, footnotesTransform } from './footnotes.js';
-export { htmlPlugin, htmlTransform, reconstructHtmlTransform } from './html.js';
+export {
+  htmlPlugin,
+  htmlTransform,
+  reconstructHtmlTransform,
+  reconstructHtmlPlugin,
+} from './html.js';
 export { htmlIdsPlugin, htmlIdsTransform } from './htmlIds.js';
 export { keysPlugin, keysTransform } from './keys.js';
 export {
diff --git a/packages/myst-transforms/tests/html.yml b/packages/myst-transforms/tests/html.yml
index 2a02aa8cf..ffab869f7 100644
--- a/packages/myst-transforms/tests/html.yml
+++ b/packages/myst-transforms/tests/html.yml
@@ -41,7 +41,6 @@ cases:
             - type: image
               url: example.jpg
               title: example
-              alt: ''
   - title: table
     before:
       type: root