diff --git a/rust/lance-datafusion/Cargo.toml b/rust/lance-datafusion/Cargo.toml
index 9a561fa9b88..36ea639e13d 100644
--- a/rust/lance-datafusion/Cargo.toml
+++ b/rust/lance-datafusion/Cargo.toml
@@ -27,7 +27,7 @@ jsonb = {workspace = true}
 lance-arrow.workspace = true
 lance-core = {workspace = true, features = ["datafusion"]}
 lance-datagen.workspace = true
-lance-geo = {workspace = true}
+lance-geo = {workspace = true, optional = true}
 chrono.workspace = true
 log.workspace = true
 pin-project.workspace = true
@@ -44,6 +44,7 @@ protobuf-src = {version = "2.1", optional = true}
 lance-datagen.workspace = true
 
 [features]
+geo = ["dep:lance-geo"]
 substrait = ["dep:datafusion-substrait"]
 protoc = ["dep:protobuf-src"]
 
diff --git a/rust/lance-datafusion/src/udf.rs b/rust/lance-datafusion/src/udf.rs
index 9117b67f82e..7d20c74071e 100644
--- a/rust/lance-datafusion/src/udf.rs
+++ b/rust/lance-datafusion/src/udf.rs
@@ -27,7 +27,52 @@ pub fn register_functions(ctx: &SessionContext) {
     ctx.register_udf(json::json_array_contains_udf());
     ctx.register_udf(json::json_array_length_udf());
     // GEO functions
+    #[cfg(feature = "geo")]
     lance_geo::register_functions(ctx);
+    #[cfg(not(feature = "geo"))]
+    register_geo_stub_functions(ctx);
+}
+
+/// When the `geo` feature is disabled, register stub UDFs for spatial SQL functions
+/// so that users get a clear error mentioning the feature flag instead of
+/// DataFusion's generic "Unknown function" error.
+#[cfg(not(feature = "geo"))]
+fn register_geo_stub_functions(ctx: &SessionContext) {
+    let geo_funcs = [
+        "st_intersects",
+        "st_contains",
+        "st_within",
+        "st_touches",
+        "st_crosses",
+        "st_overlaps",
+        "st_covers",
+        "st_coveredby",
+        "st_distance",
+        "st_area",
+        "st_length",
+    ];
+
+    for name in geo_funcs {
+        let func_name = name.to_string();
+        let stub = Arc::new(make_scalar_function(
+            move |_args: &[ArrayRef]| {
+                Err(datafusion::error::DataFusionError::Plan(format!(
+                    "Function '{}' requires the `geo` feature. \
+                     Rebuild with `--features geo` to enable geospatial functions.",
+                    func_name
+                )))
+            },
+            vec![],
+        ));
+
+        ctx.register_udf(create_udf(
+            name,
+            vec![DataType::Binary, DataType::Binary],
+            DataType::Boolean,
+            Volatility::Immutable,
+            stub,
+        ));
+    }
 }
 
 /// This method checks whether a string contains all specified tokens. The tokens are separated by
diff --git a/rust/lance-geo/Cargo.toml b/rust/lance-geo/Cargo.toml
index b8e1103027b..d8a1decfccb 100644
--- a/rust/lance-geo/Cargo.toml
+++ b/rust/lance-geo/Cargo.toml
@@ -13,13 +13,16 @@ description = "Lance's geospatial extension providing geospatial UDFs."
 
 [dependencies]
 datafusion.workspace = true
-geoarrow-array.workspace = true
-geoarrow-schema.workspace = true
-geodatafusion.workspace = true
-geo-traits.workspace = true
-geo-types.workspace = true
+geoarrow-array = { workspace = true, optional = true }
+geoarrow-schema = { workspace = true, optional = true }
+geodatafusion = { workspace = true, optional = true }
+geo-traits = { workspace = true, optional = true }
+geo-types = { workspace = true, optional = true }
 lance-core.workspace = true
 serde.workspace = true
 
+[features]
+geo = ["dep:geoarrow-array", "dep:geoarrow-schema", "dep:geodatafusion", "dep:geo-traits", "dep:geo-types"]
+
 [lints]
 workspace = true
diff --git a/rust/lance-geo/src/lib.rs b/rust/lance-geo/src/lib.rs
index 8eb562333b2..238ce3ee004 100644
--- a/rust/lance-geo/src/lib.rs
+++ b/rust/lance-geo/src/lib.rs
@@ -3,8 +3,12 @@
 
 use datafusion::prelude::SessionContext;
 
+#[cfg(feature = "geo")]
 pub mod bbox;
 
 pub fn register_functions(ctx: &SessionContext) {
+    #[cfg(feature = "geo")]
     geodatafusion::register(ctx);
+    #[cfg(not(feature = "geo"))]
+    let _ = ctx;
 }
diff --git a/rust/lance-index/Cargo.toml b/rust/lance-index/Cargo.toml
index 70262b8de92..3ce4e45ed34 100644
--- a/rust/lance-index/Cargo.toml
+++ b/rust/lance-index/Cargo.toml
@@ -30,9 +30,9 @@ deepsize.workspace = true
 dirs.workspace = true
 fst.workspace = true
 futures.workspace = true
-geoarrow-array = { workspace = true }
-geoarrow-schema = { workspace = true }
-geo-types = { workspace = true }
+geoarrow-array = { workspace = true, optional = true }
+geoarrow-schema = { workspace = true, optional = true }
+geo-types = { workspace = true, optional = true }
 half.workspace = true
 itertools.workspace = true
 jieba-rs = { workspace = true, optional = true }
@@ -42,7 +42,7 @@ lance-core.workspace = true
 lance-datafusion.workspace = true
 lance-encoding.workspace = true
 lance-file.workspace = true
-lance-geo.workspace = true
+lance-geo = { workspace = true, optional = true }
 lance-io.workspace = true
 lance-linalg.workspace = true
 lance-table.workspace = true
@@ -88,6 +88,7 @@ rstest.workspace = true
 chrono.workspace = true
 
 [features]
+geo = ["dep:lance-geo", "lance-geo/geo", "dep:geoarrow-array", "dep:geoarrow-schema", "dep:geo-types"]
 protoc = ["dep:protobuf-src"]
 tokenizer-lindera = ["dep:lindera", "dep:lindera-tantivy"]
 tokenizer-jieba = ["dep:jieba-rs"]
@@ -162,6 +163,7 @@ harness = false
 [[bench]]
 name = "geo"
 harness = false
+required-features = ["geo"]
 
 [lints]
 workspace = true
diff --git a/rust/lance-index/src/registry.rs b/rust/lance-index/src/registry.rs
index 82d24649049..0c61a0b77ce 100644
--- a/rust/lance-index/src/registry.rs
+++ b/rust/lance-index/src/registry.rs
@@ -5,13 +5,14 @@ use std::{collections::HashMap, sync::Arc};
 use lance_core::{Error, Result};
 use snafu::location;
 
+#[cfg(feature = "geo")]
+use crate::scalar::rtree::RTreeIndexPlugin;
 use crate::{
     pb, pbold,
     scalar::{
         bitmap::BitmapIndexPlugin, bloomfilter::BloomFilterIndexPlugin, btree::BTreeIndexPlugin,
         inverted::InvertedIndexPlugin, json::JsonIndexPlugin, label_list::LabelListIndexPlugin,
-        ngram::NGramIndexPlugin, registry::ScalarIndexPlugin, rtree::RTreeIndexPlugin,
-        zonemap::ZoneMapIndexPlugin,
+        ngram::NGramIndexPlugin, registry::ScalarIndexPlugin, zonemap::ZoneMapIndexPlugin,
     },
 };
 
@@ -62,6 +63,7 @@ impl IndexPluginRegistry {
         registry.add_plugin::<pb::BloomFilterIndexDetails, BloomFilterIndexPlugin>();
         registry.add_plugin::<pbold::InvertedIndexDetails, InvertedIndexPlugin>();
         registry.add_plugin::<pb::JsonIndexDetails, JsonIndexPlugin>();
+        #[cfg(feature = "geo")]
         registry.add_plugin::<pb::RTreeIndexDetails, RTreeIndexPlugin>();
 
         let registry = Arc::new(registry);
@@ -77,9 +79,17 @@ impl IndexPluginRegistry {
         self.plugins
             .get(name)
             .map(|plugin| plugin.as_ref())
-            .ok_or_else(|| Error::InvalidInput {
-                source: format!("No scalar index plugin found for name {}", name).into(),
-                location: location!(),
+            .ok_or_else(|| {
+                let hint = if name == "rtree" {
+                    ". The 'rtree' index requires the `geo` feature. \
+                     Rebuild with `--features geo` to enable geospatial support"
+                } else {
+                    ""
+                };
+                Error::InvalidInput {
+                    source: format!("No scalar index plugin found for name '{name}'{hint}").into(),
+                    location: location!(),
+                }
             })
     }
 
diff --git a/rust/lance-index/src/scalar.rs b/rust/lance-index/src/scalar.rs
index 5d7d93331b3..ead2b3bc526 100644
--- a/rust/lance-index/src/scalar.rs
+++ b/rust/lance-index/src/scalar.rs
@@ -40,6 +40,7 @@ pub mod label_list;
 pub mod lance_format;
 pub mod ngram;
 pub mod registry;
+#[cfg(feature = "geo")]
 pub mod rtree;
 pub mod zoned;
 pub mod zonemap;
@@ -736,6 +737,7 @@ impl AnyQuery for TokenQuery {
     }
 }
 
+#[cfg(feature = "geo")]
 #[derive(Debug, Clone, PartialEq)]
 pub struct RelationQuery {
     pub value: ScalarValue,
@@ -743,12 +745,14 @@ pub struct RelationQuery {
 }
 
 /// A query that a Geo index can satisfy
+#[cfg(feature = "geo")]
 #[derive(Debug, Clone, PartialEq)]
 pub enum GeoQuery {
     IntersectQuery(RelationQuery),
     IsNull,
 }
 
+#[cfg(feature = "geo")]
 impl AnyQuery for GeoQuery {
     fn as_any(&self) -> &dyn Any {
         self
diff --git a/rust/lance-index/src/scalar/expression.rs b/rust/lance-index/src/scalar/expression.rs
index 62c2cb57b8a..ec01e220115 100644
--- a/rust/lance-index/src/scalar/expression.rs
+++ b/rust/lance-index/src/scalar/expression.rs
@@ -19,9 +19,11 @@ use datafusion_expr::{
 use tokio::try_join;
 
 use super::{
-    AnyQuery, BloomFilterQuery, GeoQuery, LabelListQuery, MetricsCollector, RelationQuery,
-    SargableQuery, ScalarIndex, SearchResult, TextQuery, TokenQuery,
+    AnyQuery, BloomFilterQuery, LabelListQuery, MetricsCollector, SargableQuery, ScalarIndex,
+    SearchResult, TextQuery, TokenQuery,
 };
+#[cfg(feature = "geo")]
+use super::{GeoQuery, RelationQuery};
 use lance_core::{
     utils::mask::{NullableRowAddrMask, RowAddrMask},
     Error, Result,
@@ -692,17 +694,20 @@ impl ScalarQueryParser for FtsQueryParser {
 }
 
 /// A parser for geo indices that handles spatial queries
+#[cfg(feature = "geo")]
 #[derive(Debug, Clone)]
 pub struct GeoQueryParser {
     index_name: String,
 }
 
+#[cfg(feature = "geo")]
 impl GeoQueryParser {
     pub fn new(index_name: String) -> Self {
         Self { index_name }
     }
 }
 
+#[cfg(feature = "geo")]
 impl ScalarQueryParser for GeoQueryParser {
     fn visit_between(
         &self,
diff --git a/rust/lance/Cargo.toml b/rust/lance/Cargo.toml
index 427de2aa30e..f630905369a 100644
--- a/rust/lance/Cargo.toml
+++ b/rust/lance/Cargo.toml
@@ -26,7 +26,7 @@ lance-linalg = { workspace = true }
 lance-index = { workspace = true }
 lance-namespace = { workspace = true }
 lance-table = { workspace = true }
-lance-geo = { workspace = true }
+lance-geo = { workspace = true, optional = true }
 arrow-arith = { workspace = true }
 arrow-array = { workspace = true }
 arrow-buffer = { workspace = true }
@@ -119,7 +119,7 @@ geo-types = { workspace = true }
 datafusion-substrait = { workspace = true }
 
 [features]
-default = ["aws", "azure", "gcp", "oss", "huggingface", "tencent"]
+default = ["aws", "azure", "gcp", "oss", "huggingface", "tencent", "geo"]
 fp16kernels = ["lance-linalg/fp16kernels"]
 # Prevent dynamic linking of lzma, which comes from datafusion
 cli = ["dep:clap", "lzma-sys/static"]
@@ -138,6 +138,7 @@ azure = ["lance-io/azure"]
 oss = ["lance-io/oss"]
 tencent = ["lance-io/tencent"]
 huggingface = ["lance-io/huggingface"]
+geo = ["dep:lance-geo", "lance-geo/geo", "lance-datafusion/geo", "lance-index/geo"]
 # Enable slow integration tests (disabled by default in CI)
 slow_tests = []
 
diff --git a/rust/lance/src/dataset/tests/mod.rs b/rust/lance/src/dataset/tests/mod.rs
index c0a6002debb..ecc64587b0c 100644
--- a/rust/lance/src/dataset/tests/mod.rs
+++ b/rust/lance/src/dataset/tests/mod.rs
@@ -5,6 +5,7 @@
 mod dataset_aggregate;
 mod dataset_common;
 mod dataset_concurrency_store;
+#[cfg(feature = "geo")]
 mod dataset_geo;
 mod dataset_index;
 mod dataset_io;
diff --git a/rust/lance/src/index.rs b/rust/lance/src/index.rs
index 6d846cff4a5..828374e4d11 100644
--- a/rust/lance/src/index.rs
+++ b/rust/lance/src/index.rs
@@ -292,9 +292,22 @@ pub(crate) async fn remap_index(
 
     let new_id = Uuid::new_v4();
 
-    let generic = dataset
+    let generic = match dataset
         .open_generic_index(&field_path, &index_id.to_string(), &NoOpMetricsCollector)
-        .await?;
+        .await
+    {
+        Ok(g) => g,
+        Err(e) => {
+            log::warn!(
+                "Cannot open index '{}' on '{}': {}. \
+                 Index will be dropped during compaction.",
+                index_id,
+                field_path,
+                e
+            );
+            return Ok(RemapResult::Drop);
+        }
+    };
 
     let created_index = match generic.index_type() {
         it if it.is_scalar() => {
@@ -1718,7 +1731,19 @@ impl DatasetIndexInternalExt for Dataset {
                 continue;
             }
 
-            let plugin = index_details.get_plugin()?;
+            let plugin = match index_details.get_plugin() {
+                Ok(plugin) => plugin,
+                Err(e) => {
+                    log::warn!(
+                        "Skipping index '{}' on column '{}': {}. \
+                         Queries on this column will fall back to a full scan.",
+                        index.name,
+                        field_path,
+                        e
+                    );
+                    continue;
+                }
+            };
             let query_parser = plugin.new_query_parser(index.name.clone(), &index_details.0);
 
             if let Some(query_parser) = query_parser {
diff --git a/rust/lance/src/index/append.rs b/rust/lance/src/index/append.rs
index f03503fb61d..e552afcaa8f 100644
--- a/rust/lance/src/index/append.rs
+++ b/rust/lance/src/index/append.rs
@@ -87,10 +87,21 @@ pub async fn merge_indices_with_unindexed_frags<'a>(
     let field_path = dataset.schema().field_path(old_indices[0].fields[0])?;
     let mut indices = Vec::with_capacity(old_indices.len());
     for idx in old_indices {
-        let index = dataset
+        match dataset
             .open_generic_index(&field_path, &idx.uuid.to_string(), &NoOpMetricsCollector)
-            .await?;
-        indices.push(index);
+            .await
+        {
+            Ok(index) => indices.push(index),
+            Err(e) => {
+                log::warn!(
+                    "Cannot open index on column '{}': {}. \
+                     Skipping index merge for this column.",
+                    field_path,
+                    e
+                );
+                return Ok(None);
+            }
+        }
     }
 
     if indices