diff --git a/CHANGELOG.md b/CHANGELOG.md
index 82efa7c0..389ade58 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -13,11 +13,17 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - Report diagnostics for unused BibTeX entries and undefined citations
 - Report diagnostics for duplicate BibTeX entries
 - Report diagnostics for duplicate labels
+- Add `texlab.build.auxDirectory` and `texlab.build.logDirectory` settings ([#906](https://github.com/latex-lsp/texlab/issues/906))
+
+### Deprecated
+
+- Deprecate `texlab.auxDirectory` in favor of `texlab.build.auxDirectory`
 
 ### Fixed
 
 - Fix parsing paths with `|` ([#568](https://github.com/latex-lsp/texlab/issues/568))
 - Fix parsing LaTeX identifiers with `=` ([#568](https://github.com/latex-lsp/texlab/issues/568))
+- Fix search path for aux files when using `\include` instead of `\input` ([[#906](https://github.com/latex-lsp/texlab/issues/906))
 
 ## [5.7.0] - 2023-06-07
 
diff --git a/crates/base-db/src/config.rs b/crates/base-db/src/config.rs
index 0ffd78c6..36063b47 100644
--- a/crates/base-db/src/config.rs
+++ b/crates/base-db/src/config.rs
@@ -22,7 +22,8 @@ pub struct BuildConfig {
     pub args: Vec<String>,
     pub on_save: bool,
     pub forward_search_after: bool,
-    pub output_dir: String,
+    pub aux_dir: String,
+    pub log_dir: String,
     pub output_filename: Option<PathBuf>,
 }
 
@@ -112,7 +113,8 @@ impl Default for BuildConfig {
                 .collect(),
             on_save: false,
             forward_search_after: false,
-            output_dir: String::from("."),
+            aux_dir: String::from("."),
+            log_dir: String::from("."),
             output_filename: None,
         }
     }
diff --git a/crates/base-db/src/data.rs b/crates/base-db/src/data.rs
index dac0b49a..64313c0e 100644
--- a/crates/base-db/src/data.rs
+++ b/crates/base-db/src/data.rs
@@ -25,13 +25,13 @@ pub struct BibtexFieldType<'a> {
 impl<'a> BibtexEntryType<'a> {
     pub fn find(name: &str) -> Option<Self> {
         BIBTEX_ENTRY_TYPES.iter().find(|ty| ty.name.eq_ignore_ascii_case(name)).copied()
-    }    
+    }
 }
 
 impl<'a> BibtexFieldType<'a> {
     pub fn find(name: &str) -> Option<Self> {
         BIBTEX_FIELD_TYPES.iter().find(|ty| ty.name.eq_ignore_ascii_case(name)).copied()
-    }    
+    }
 }
 
 
diff --git a/crates/base-db/src/graph.rs b/crates/base-db/src/graph.rs
index 5e727d2b..3e718afd 100644
--- a/crates/base-db/src/graph.rs
+++ b/crates/base-db/src/graph.rs
@@ -48,15 +48,18 @@ impl<'a> Graph<'a> {
 
         while let Some((source, base_dir)) = stack.pop() {
             let index = graph.edges.len();
-            graph.explicit_edges(source, &base_dir);
+            graph.add_explicit_edges(source, &base_dir);
             for edge in &graph.edges[index..] {
-                let Some(weight) = edge.weight.as_ref() else { continue };
+                let Some(weight) = edge.weight.as_ref() else {
+                    continue;
+                };
+
                 if visited.insert(&edge.target.uri) {
                     stack.push((edge.target, weight.new_base_dir.clone()));
                 }
             }
 
-            graph.implicit_edges(source, &base_dir);
+            graph.add_implicit_edges(source, &base_dir);
         }
 
         graph
@@ -68,19 +71,17 @@ impl<'a> Graph<'a> {
             .unique_by(|document| &document.uri)
     }
 
-    fn explicit_edges(&mut self, source: &'a Document, base_dir: &Url) {
-        let DocumentData::Tex(data) = &source.data else { return };
+    fn add_explicit_edges(&mut self, source: &'a Document, base_dir: &Url) {
+        let DocumentData::Tex(data) = &source.data else {
+            return;
+        };
+
         for link in &data.semantics.links {
-            self.explicit_edge(source, base_dir, link);
+            self.add_link(source, base_dir, link);
         }
     }
 
-    fn explicit_edge(
-        &mut self,
-        source: &'a Document,
-        base_dir: &Url,
-        link: &'a semantics::tex::Link,
-    ) {
+    fn add_link(&mut self, source: &'a Document, base_dir: &Url, link: &'a semantics::tex::Link) {
         let home_dir = HOME_DIR.as_deref();
 
         let stem = &link.path.text;
@@ -130,15 +131,20 @@ impl<'a> Graph<'a> {
         }
     }
 
-    fn implicit_edges(&mut self, source: &'a Document, base_dir: &Url) {
-        let uri = source.uri.as_str();
-        if source.language == Language::Tex && !uri.ends_with(".aux") {
-            self.implicit_edge(source, base_dir, "log");
-            self.implicit_edge(source, base_dir, "aux");
+    fn add_implicit_edges(&mut self, source: &'a Document, base_dir: &Url) {
+        if source.language == Language::Tex {
+            let config = &self.workspace.config().build;
+            let aux_dir = self.workspace.output_dir(base_dir, config.aux_dir.clone());
+            let log_dir = self.workspace.output_dir(base_dir, config.log_dir.clone());
+
+            self.add_artifact(source, &aux_dir, "aux");
+            self.add_artifact(source, base_dir, "aux");
+            self.add_artifact(source, &log_dir, "log");
+            self.add_artifact(source, base_dir, "log");
         }
     }
 
-    fn implicit_edge(&mut self, source: &'a Document, base_dir: &Url, extension: &str) {
+    fn add_artifact(&mut self, source: &'a Document, base_dir: &Url, extension: &str) {
         let mut path = PathBuf::from(
             percent_decode_str(source.uri.path())
                 .decode_utf8_lossy()
@@ -146,9 +152,13 @@ impl<'a> Graph<'a> {
         );
 
         path.set_extension(extension);
-        let Some(target_uri) = path.file_name()
+        let Some(target_uri) = path
+            .file_name()
             .and_then(OsStr::to_str)
-            .and_then(|name| self.workspace.output_dir(base_dir).join(name).ok()) else { return };
+            .and_then(|name| base_dir.join(name).ok())
+        else {
+            return;
+        };
 
         match self.workspace.lookup(&target_uri) {
             Some(target) => {
diff --git a/crates/base-db/src/workspace.rs b/crates/base-db/src/workspace.rs
index 15d29de8..9308c240 100644
--- a/crates/base-db/src/workspace.rs
+++ b/crates/base-db/src/workspace.rs
@@ -109,9 +109,22 @@ impl Workspace {
         self.iter()
             .filter(|document| document.uri.scheme() == "file")
             .flat_map(|document| {
-                let dir1 = self.output_dir(&self.current_dir(&document.dir));
-                let dir2 = &document.dir;
-                [dir1.to_file_path(), dir2.to_file_path()]
+                let dir1 = self.output_dir(
+                    &self.current_dir(&document.dir),
+                    self.config.build.aux_dir.clone(),
+                );
+
+                let dir2 = self.output_dir(
+                    &self.current_dir(&document.dir),
+                    self.config.build.log_dir.clone(),
+                );
+
+                let dir3 = &document.dir;
+                [
+                    dir1.to_file_path(),
+                    dir2.to_file_path(),
+                    dir3.to_file_path(),
+                ]
             })
             .flatten()
             .for_each(|path| {
@@ -135,8 +148,8 @@ impl Workspace {
             .unwrap_or_else(|| base_dir.clone())
     }
 
-    pub fn output_dir(&self, base_dir: &Url) -> Url {
-        let mut path = self.config.build.output_dir.clone();
+    pub fn output_dir(&self, base_dir: &Url, relative_path: String) -> Url {
+        let mut path = relative_path;
         if !path.ends_with('/') {
             path.push('/');
         }
@@ -168,7 +181,9 @@ impl Workspace {
     pub fn parents(&self, child: &Document) -> FxHashSet<&Document> {
         self.iter()
             .filter(|document| {
-                let DocumentData::Tex(data) = &document.data else { return false };
+                let DocumentData::Tex(data) = &document.data else {
+                    return false;
+                };
                 data.semantics.can_be_root
             })
             .filter(|parent| {
@@ -264,14 +279,18 @@ impl Workspace {
                 continue;
             }
 
-            let Ok(entries) = std::fs::read_dir(dir) else { continue };
+            let Ok(entries) = std::fs::read_dir(dir) else {
+                continue;
+            };
 
             for file in entries
                 .flatten()
                 .filter(|entry| entry.file_type().map_or(false, |type_| type_.is_file()))
                 .map(|entry| entry.path())
             {
-                let Some(lang) = Language::from_path(&file) else { continue };
+                let Some(lang) = Language::from_path(&file) else {
+                    continue;
+                };
                 if !matches!(lang, Language::Tex | Language::Root | Language::Tectonic) {
                     continue;
                 }
diff --git a/crates/commands/src/clean.rs b/crates/commands/src/clean.rs
index 391be79c..d6c3977f 100644
--- a/crates/commands/src/clean.rs
+++ b/crates/commands/src/clean.rs
@@ -22,7 +22,10 @@ impl CleanCommand {
         };
 
         let dir = workspace.current_dir(&document.dir);
-        let dir = workspace.output_dir(&dir).to_file_path().unwrap();
+        let dir = workspace
+            .output_dir(&dir, workspace.config().build.log_dir.clone())
+            .to_file_path()
+            .unwrap();
 
         let flag = match target {
             CleanTarget::Auxiliary => "-c",
diff --git a/crates/commands/src/fwd_search.rs b/crates/commands/src/fwd_search.rs
index 3669a289..153e1245 100644
--- a/crates/commands/src/fwd_search.rs
+++ b/crates/commands/src/fwd_search.rs
@@ -59,7 +59,10 @@ impl ForwardSearch {
         }
 
         let dir = workspace.current_dir(&parent.dir);
-        let dir = workspace.output_dir(&dir).to_file_path().unwrap();
+        let dir = workspace
+            .output_dir(&dir, workspace.config().build.log_dir.clone())
+            .to_file_path()
+            .unwrap();
 
         let Some(tex_path) = &child.path else {
             return Err(ForwardSearchError::InvalidPath(child.uri.clone()));
@@ -67,11 +70,12 @@ impl ForwardSearch {
 
         let override_path = workspace.config().build.output_filename.as_deref();
 
-        let Some(pdf_path) = override_path.or(parent.path.as_deref())
+        let Some(pdf_path) = override_path
+            .or(parent.path.as_deref())
             .and_then(Path::file_stem)
             .and_then(OsStr::to_str)
-            .map(|stem| dir.join(format!("{stem}.pdf"))) else 
-        {
+            .map(|stem| dir.join(format!("{stem}.pdf")))
+        else {
             return Err(ForwardSearchError::InvalidPath(parent.uri.clone()));
         };
 
diff --git a/crates/texlab/src/server/options.rs b/crates/texlab/src/server/options.rs
index af20c313..ddf20f0a 100644
--- a/crates/texlab/src/server/options.rs
+++ b/crates/texlab/src/server/options.rs
@@ -69,6 +69,8 @@ pub struct BuildOptions {
     pub args: Option<Vec<String>>,
     pub on_save: bool,
     pub forward_search_after: bool,
+    pub aux_directory: Option<String>,
+    pub log_directory: Option<String>,
     pub filename: Option<String>,
 }
 
@@ -155,7 +157,19 @@ impl From<Options> for Config {
         config.build.args = value.build.args.unwrap_or(config.build.args);
         config.build.on_save = value.build.on_save;
         config.build.forward_search_after = value.build.forward_search_after;
-        config.build.output_dir = value.aux_directory.unwrap_or_else(|| String::from("."));
+
+        config.build.aux_dir = value
+            .build
+            .aux_directory
+            .or_else(|| value.aux_directory.clone())
+            .unwrap_or_else(|| String::from("."));
+
+        config.build.log_dir = value
+            .build
+            .log_directory
+            .or_else(|| value.aux_directory)
+            .unwrap_or_else(|| String::from("."));
+
         config.build.output_filename = value.build.filename.map(PathBuf::from);
 
         config.diagnostics.allowed_patterns = value