diff --git a/Cargo.lock b/Cargo.lock
index 695b4cc9fa81..68b4cc0adc06 100644
--- a/Cargo.lock
+++ b/Cargo.lock
@@ -52,9 +52,9 @@ dependencies = [
 
 [[package]]
 name = "addr2line"
-version = "0.24.2"
+version = "0.25.1"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "dfbe277e56a376000877090da837660b4427aad530e3028d44e0bffe4f89a1c1"
+checksum = "1b5d307320b3181d6d7954e663bd7c774a838b8220fe0593c86d9fb09f498b4b"
 dependencies = [
  "gimli",
 ]
@@ -152,9 +152,9 @@ dependencies = [
 
 [[package]]
 name = "anstyle"
-version = "1.0.11"
+version = "1.0.13"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "862ed96ca487e809f1c8e5a8447f6ee2cf102f846893800b20cebdf541fc6bbd"
+checksum = "5192cca8006f1fd4f7237516f40fa183bb07f8fbdfedaa0036de5ea9b0b45e78"
 
 [[package]]
 name = "anstyle-parse"
@@ -616,9 +616,9 @@ dependencies = [
 
 [[package]]
 name = "aws-lc-rs"
-version = "1.14.0"
+version = "1.14.1"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "94b8ff6c09cd57b16da53641caa860168b88c172a5ee163b0288d3d6eea12786"
+checksum = "879b6c89592deb404ba4dc0ae6b58ffd1795c78991cbb5b8bc441c48a070440d"
 dependencies = [
  "aws-lc-sys",
  "zeroize",
@@ -626,15 +626,16 @@ dependencies = [
 
 [[package]]
 name = "aws-lc-sys"
-version = "0.31.0"
+version = "0.32.2"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "0e44d16778acaf6a9ec9899b92cebd65580b83f685446bf2e1f5d3d732f99dcd"
+checksum = "a2b715a6010afb9e457ca2b7c9d2b9c344baa8baed7b38dc476034c171b32575"
 dependencies = [
  "bindgen",
  "cc",
  "cmake",
  "dunce",
  "fs_extra",
+ "libloading 0.8.8",
 ]
 
 [[package]]
@@ -685,9 +686,9 @@ dependencies = [
 
 [[package]]
 name = "aws-sdk-ssooidc"
-version = "1.85.0"
+version = "1.86.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "67e05f33b6c9026fecfe9b3b6740f34d41bc6ff641a6a32dabaab60209245b75"
+checksum = "9d1cc7fb324aa12eb4404210e6381195c5b5e9d52c2682384f295f38716dd3c7"
 dependencies = [
  "aws-credential-types",
  "aws-runtime",
@@ -783,9 +784,9 @@ dependencies = [
 
 [[package]]
 name = "aws-smithy-http-client"
-version = "1.1.1"
+version = "1.1.2"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "147e8eea63a40315d704b97bf9bc9b8c1402ae94f89d5ad6f7550d963309da1b"
+checksum = "734b4282fbb7372923ac339cc2222530f8180d9d4745e582de19a18cee409fd8"
 dependencies = [
  "aws-smithy-async",
  "aws-smithy-runtime-api",
@@ -922,9 +923,9 @@ dependencies = [
 
 [[package]]
 name = "axum"
-version = "0.8.4"
+version = "0.8.6"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "021e862c184ae977658b36c4500f7feac3221ca5da43e3f25bd04ab6c79a29b5"
+checksum = "8a18ed336352031311f4e0b4dd2ff392d4fbb370777c9d18d7fc9d7359f73871"
 dependencies = [
  "axum-core",
  "bytes",
@@ -938,8 +939,7 @@ dependencies = [
  "mime",
  "percent-encoding",
  "pin-project-lite",
- "rustversion",
- "serde",
+ "serde_core",
  "sync_wrapper",
  "tower",
  "tower-layer",
@@ -948,9 +948,9 @@ dependencies = [
 
 [[package]]
 name = "axum-core"
-version = "0.5.2"
+version = "0.5.5"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "68464cd0412f486726fb3373129ef5d2993f90c34bc2bc1c1e9943b2f4fc7ca6"
+checksum = "59446ce19cd142f8833f856eb31f3eb097812d1479ab224f54d72428ca21ea22"
 dependencies = [
  "bytes",
  "futures-core",
@@ -959,7 +959,6 @@ dependencies = [
  "http-body-util",
  "mime",
  "pin-project-lite",
- "rustversion",
  "sync_wrapper",
  "tower-layer",
  "tower-service",
@@ -967,9 +966,9 @@ dependencies = [
 
 [[package]]
 name = "backtrace"
-version = "0.3.75"
+version = "0.3.76"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "6806a6321ec58106fea15becdad98371e28d92ccbc7c8f1b3b6dd724fe8f1002"
+checksum = "bb531853791a215d7c62a30daf0dde835f381ab5de4589cfe7c649d2cbe92bd6"
 dependencies = [
  "addr2line",
  "cfg-if",
@@ -977,7 +976,7 @@ dependencies = [
  "miniz_oxide",
  "object",
  "rustc-demangle",
- "windows-targets 0.52.6",
+ "windows-link 0.2.0",
 ]
 
 [[package]]
@@ -1306,9 +1305,9 @@ checksum = "37b2a672a2cb129a2e41c10b1224bb368f9f37a2b16b612598138befd7b37eb5"
 
 [[package]]
 name = "cc"
-version = "1.2.38"
+version = "1.2.39"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "80f41ae168f955c12fb8960b057d70d0ca153fb83182b57d86380443527be7e9"
+checksum = "e1354349954c6fc9cb0deab020f27f783cf0b604e8bb754dc4658ecf0d29c35f"
 dependencies = [
  "find-msvc-tools",
  "jobserver",
@@ -1396,7 +1395,7 @@ checksum = "0b023947811758c97c59bf9d1c188fd619ad4718dcaa767947df1cadb14f39f4"
 dependencies = [
  "glob",
  "libc",
- "libloading 0.8.9",
+ "libloading 0.8.8",
 ]
 
 [[package]]
@@ -1507,7 +1506,7 @@ dependencies = [
  "libc",
  "once_cell",
  "unicode-width 0.2.1",
- "windows-sys 0.61.0",
+ "windows-sys 0.61.1",
 ]
 
 [[package]]
@@ -2512,7 +2511,7 @@ dependencies = [
  "datafusion-proto-common",
  "doc-comment",
  "object_store",
- "pbjson",
+ "pbjson 0.7.0",
  "pretty_assertions",
  "prost 0.13.5",
  "serde",
@@ -2527,7 +2526,7 @@ dependencies = [
  "arrow",
  "datafusion-common",
  "doc-comment",
- "pbjson",
+ "pbjson 0.7.0",
  "prost 0.13.5",
  "serde",
 ]
@@ -2654,7 +2653,7 @@ dependencies = [
  "itertools 0.14.0",
  "object_store",
  "pbjson-types",
- "prost 0.13.5",
+ "prost 0.14.1",
  "serde_json",
  "substrait",
  "tokio",
@@ -2685,12 +2684,12 @@ dependencies = [
 
 [[package]]
 name = "deranged"
-version = "0.5.3"
+version = "0.5.4"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "d630bccd429a5bb5a64b5e94f693bfc48c9f8566418fda4c494cc94f911f87cc"
+checksum = "a41953f86f8a05768a6cda24def994fd2f424b04ec5c719cf89989779f199071"
 dependencies = [
  "powerfmt",
- "serde",
+ "serde_core",
 ]
 
 [[package]]
@@ -2728,7 +2727,7 @@ dependencies = [
  "libc",
  "option-ext",
  "redox_users",
- "windows-sys 0.61.0",
+ "windows-sys 0.61.1",
 ]
 
 [[package]]
@@ -2872,7 +2871,7 @@ source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "39cab71617ae0d63f51a36d69f866391735b51691dbda63cf6f96d042b63efeb"
 dependencies = [
  "libc",
- "windows-sys 0.61.0",
+ "windows-sys 0.61.1",
 ]
 
 [[package]]
@@ -2977,9 +2976,9 @@ checksum = "1d674e81391d1e1ab681a28d99df07927c6d4aa5b027d7da16ba32d1d21ecd99"
 
 [[package]]
 name = "flatbuffers"
-version = "25.2.10"
+version = "25.9.23"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "1045398c1bfd89168b5fd3f1fc11f6e70b34f6f66300c87d44d3de849463abf1"
+checksum = "09b6620799e7340ebd9968d2e0708eb82cf1971e9a16821e2091b6d6e475eed5"
 dependencies = [
  "bitflags 2.9.4",
  "rustc_version",
@@ -3137,16 +3136,16 @@ dependencies = [
 name = "gen"
 version = "0.1.0"
 dependencies = [
- "pbjson-build 0.8.0",
- "prost-build 0.14.1",
+ "pbjson-build",
+ "prost-build",
 ]
 
 [[package]]
 name = "gen-common"
 version = "0.1.0"
 dependencies = [
- "pbjson-build 0.8.0",
- "prost-build 0.14.1",
+ "pbjson-build",
+ "prost-build",
 ]
 
 [[package]]
@@ -3197,9 +3196,9 @@ dependencies = [
 
 [[package]]
 name = "gimli"
-version = "0.31.1"
+version = "0.32.3"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "07e28edb80900c19c28f1072f2e8aeca7fa06b23cd4169cefe1af5aa3260783f"
+checksum = "e629b9b98ef3dd8afe6ca2bd0f89306cec16d43d907889945bc5d6687f2f13c7"
 
 [[package]]
 name = "glob"
@@ -3524,7 +3523,7 @@ dependencies = [
  "js-sys",
  "log",
  "wasm-bindgen",
- "windows-core 0.62.0",
+ "windows-core 0.62.1",
 ]
 
 [[package]]
@@ -3931,12 +3930,12 @@ dependencies = [
 
 [[package]]
 name = "libloading"
-version = "0.8.9"
+version = "0.8.8"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "d7c4b02199fee7c5d21a5ae7d8cfa79a6ef5bb2fc834d6e9058e89c825efdc55"
+checksum = "07033963ba89ebaf1584d767badaa2e8fcec21aedea6b8c0346d487d49c28667"
 dependencies = [
  "cfg-if",
- "windows-link 0.2.0",
+ "windows-targets 0.53.4",
 ]
 
 [[package]]
@@ -4060,9 +4059,9 @@ dependencies = [
 
 [[package]]
 name = "memchr"
-version = "2.7.5"
+version = "2.7.6"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "32a282da65faaf38286cf3be983213fcf1d2e2a58700e808f83f4ea9a4804bc0"
+checksum = "f52b00d39961fc5b2736ea853c9cc86238e165017a493d1d5c8eac6bdc4cc273"
 
 [[package]]
 name = "memoffset"
@@ -4281,9 +4280,9 @@ dependencies = [
 
 [[package]]
 name = "object"
-version = "0.36.7"
+version = "0.37.3"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "62948e14d923ea95ea2c7c86c71013138b66525b86bdc08d2dcc262bdb497b87"
+checksum = "ff76201f031d8863c38aa7f905eca4f53abbfa15f609db4277d44cd8938f33fe"
 dependencies = [
  "memchr",
 ]
@@ -4372,9 +4371,9 @@ checksum = "1a80800c0488c3a21695ea981a54918fbb37abf04f4d0720c453632255e2ff0e"
 
 [[package]]
 name = "owo-colors"
-version = "4.2.2"
+version = "4.2.3"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "48dd4f4a2c8405440fd0462561f0e5806bd0f77e86f51c761481bdd4018b545e"
+checksum = "9c6901729fa79e91a0913333229e9ca5dc725089d1c363b2f4b4760709dc4a52"
 
 [[package]]
 name = "parking_lot"
@@ -4478,15 +4477,13 @@ dependencies = [
 ]
 
 [[package]]
-name = "pbjson-build"
-version = "0.7.0"
+name = "pbjson"
+version = "0.8.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "6eea3058763d6e656105d1403cb04e0a41b7bbac6362d413e7c33be0c32279c9"
+checksum = "898bac3fa00d0ba57a4e8289837e965baa2dee8c3749f3b11d45a64b4223d9c3"
 dependencies = [
- "heck 0.5.0",
- "itertools 0.13.0",
- "prost 0.13.5",
- "prost-types 0.13.5",
+ "base64 0.22.1",
+ "serde",
 ]
 
 [[package]]
@@ -4503,16 +4500,16 @@ dependencies = [
 
 [[package]]
 name = "pbjson-types"
-version = "0.7.0"
+version = "0.8.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "e54e5e7bfb1652f95bc361d76f3c780d8e526b134b85417e774166ee941f0887"
+checksum = "8e748e28374f10a330ee3bb9f29b828c0ac79831a32bab65015ad9b661ead526"
 dependencies = [
  "bytes",
  "chrono",
- "pbjson",
- "pbjson-build 0.7.0",
- "prost 0.13.5",
- "prost-build 0.13.5",
+ "pbjson 0.8.0",
+ "pbjson-build",
+ "prost 0.14.1",
+ "prost-build",
  "serde",
 ]
 
@@ -4811,26 +4808,6 @@ dependencies = [
  "prost-derive 0.14.1",
 ]
 
-[[package]]
-name = "prost-build"
-version = "0.13.5"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "be769465445e8c1474e9c5dac2018218498557af32d9ed057325ec9a41ae81bf"
-dependencies = [
- "heck 0.5.0",
- "itertools 0.14.0",
- "log",
- "multimap",
- "once_cell",
- "petgraph 0.7.1",
- "prettyplease",
- "prost 0.13.5",
- "prost-types 0.13.5",
- "regex",
- "syn 2.0.106",
- "tempfile",
-]
-
 [[package]]
 name = "prost-build"
 version = "0.14.1"
@@ -5237,18 +5214,18 @@ dependencies = [
 
 [[package]]
 name = "ref-cast"
-version = "1.0.24"
+version = "1.0.25"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "4a0ae411dbe946a674d89546582cea4ba2bb8defac896622d6496f14c23ba5cf"
+checksum = "f354300ae66f76f1c85c5f84693f0ce81d747e2c3f21a45fef496d89c960bf7d"
 dependencies = [
  "ref-cast-impl",
 ]
 
 [[package]]
 name = "ref-cast-impl"
-version = "1.0.24"
+version = "1.0.25"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "1165225c21bff1f3bbce98f5a1f889949bc902d3575308cc7b0de30b4f6d27c7"
+checksum = "b7186006dcb21920990093f30e3dea63b7d6e977bf1256be20c3563a5db070da"
 dependencies = [
  "proc-macro2",
  "quote",
@@ -5498,7 +5475,7 @@ dependencies = [
  "errno",
  "libc",
  "linux-raw-sys",
- "windows-sys 0.61.0",
+ "windows-sys 0.61.1",
 ]
 
 [[package]]
@@ -5549,9 +5526,9 @@ dependencies = [
 
 [[package]]
 name = "rustls-webpki"
-version = "0.103.6"
+version = "0.103.7"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "8572f3c2cb9934231157b45499fc41e1f58c589fdfb81a844ba873265e80f8eb"
+checksum = "e10b3f4191e8a80e6b43eebabfac91e5dcecebb27a71f04e820c47ec41d314bf"
 dependencies = [
  "aws-lc-rs",
  "ring",
@@ -5608,7 +5585,7 @@ version = "0.1.28"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "891d81b926048e76efe18581bf793546b4c0eaf8448d72be8de2bbee5fd166e1"
 dependencies = [
- "windows-sys 0.61.0",
+ "windows-sys 0.61.1",
 ]
 
 [[package]]
@@ -5673,9 +5650,9 @@ checksum = "1c107b6f4780854c8b126e228ea8869f4d7b71260f962fefb57b996b8959ba6b"
 
 [[package]]
 name = "security-framework"
-version = "3.5.0"
+version = "3.5.1"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "cc198e42d9b7510827939c9a15f5062a0c913f3371d765977e586d2fe6c16f4a"
+checksum = "b3297343eaf830f66ede390ea39da1d462b6b0c1b000f420d0a83f898bbbe6ef"
 dependencies = [
  "bitflags 2.9.4",
  "core-foundation",
@@ -6153,18 +6130,18 @@ dependencies = [
 
 [[package]]
 name = "substrait"
-version = "0.58.0"
+version = "0.60.1"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "de6d24c270c6c672a86c183c3a8439ba46c1936f93cf7296aa692de3b0ff0228"
+checksum = "3ab275be098c14876dbe7c15b65803e99ad19b52075232c142ec4019f5945e5b"
 dependencies = [
  "heck 0.5.0",
- "pbjson",
- "pbjson-build 0.7.0",
+ "pbjson 0.8.0",
+ "pbjson-build",
  "pbjson-types",
  "prettyplease",
- "prost 0.13.5",
- "prost-build 0.13.5",
- "prost-types 0.13.5",
+ "prost 0.14.1",
+ "prost-build",
+ "prost-types 0.14.1",
  "protobuf-src",
  "regress",
  "schemars 0.8.22",
@@ -6261,7 +6238,7 @@ dependencies = [
  "getrandom 0.3.3",
  "once_cell",
  "rustix",
- "windows-sys 0.61.0",
+ "windows-sys 0.61.1",
 ]
 
 [[package]]
@@ -6496,9 +6473,9 @@ dependencies = [
 
 [[package]]
 name = "tokio-rustls"
-version = "0.26.3"
+version = "0.26.4"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "05f63835928ca123f1bef57abbcd23bb2ba0ac9ae1235f1e65bda0d06e7786bd"
+checksum = "1729aa945f29d91ba541258c8df89027d5792d85a8841fb65e8bf0f4ede4ef61"
 dependencies = [
  "rustls",
  "tokio",
@@ -7140,7 +7117,7 @@ version = "0.1.11"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "c2a7b1c03c876122aa43f3020e6c3c3ee5c05081c9a00739faf7503aeba10d22"
 dependencies = [
- "windows-sys 0.61.0",
+ "windows-sys 0.61.1",
 ]
 
 [[package]]
@@ -7186,9 +7163,9 @@ dependencies = [
 
 [[package]]
 name = "windows-core"
-version = "0.62.0"
+version = "0.62.1"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "57fe7168f7de578d2d8a05b07fd61870d2e73b4020e9f49aa00da8471723497c"
+checksum = "6844ee5416b285084d3d3fffd743b925a6c9385455f64f6d4fa3031c4c2749a9"
 dependencies = [
  "windows-implement",
  "windows-interface",
@@ -7210,9 +7187,9 @@ dependencies = [
 
 [[package]]
 name = "windows-implement"
-version = "0.60.0"
+version = "0.60.1"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "a47fddd13af08290e67f4acabf4b459f647552718f683a7b415d290ac744a836"
+checksum = "edb307e42a74fb6de9bf3a02d9712678b22399c87e6fa869d6dfcd8c1b7754e0"
 dependencies = [
  "proc-macro2",
  "quote",
@@ -7221,9 +7198,9 @@ dependencies = [
 
 [[package]]
 name = "windows-interface"
-version = "0.59.1"
+version = "0.59.2"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "bd9211b69f8dcdfa817bfd14bf1c97c9188afa36f4750130fcdf3f400eca9fa8"
+checksum = "c0abd1ddbc6964ac14db11c7213d6532ef34bd9aa042c2e5935f59d7908b46a5"
 dependencies = [
  "proc-macro2",
  "quote",
@@ -7312,14 +7289,14 @@ version = "0.60.2"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "f2f500e4d28234f72040990ec9d39e3a6b950f9f22d3dba18416c35882612bcb"
 dependencies = [
- "windows-targets 0.53.3",
+ "windows-targets 0.53.4",
 ]
 
 [[package]]
 name = "windows-sys"
-version = "0.61.0"
+version = "0.61.1"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "e201184e40b2ede64bc2ea34968b28e33622acdbbf37104f0e4a33f7abe657aa"
+checksum = "6f109e41dd4a3c848907eb83d5a42ea98b3769495597450cf6d153507b166f0f"
 dependencies = [
  "windows-link 0.2.0",
 ]
@@ -7342,11 +7319,11 @@ dependencies = [
 
 [[package]]
 name = "windows-targets"
-version = "0.53.3"
+version = "0.53.4"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "d5fe6031c4041849d7c496a8ded650796e7b6ecc19df1a431c1a363342e5dc91"
+checksum = "2d42b7b7f66d2a06854650af09cfdf8713e427a439c97ad65a6375318033ac4b"
 dependencies = [
- "windows-link 0.1.3",
+ "windows-link 0.2.0",
  "windows_aarch64_gnullvm 0.53.0",
  "windows_aarch64_msvc 0.53.0",
  "windows_i686_gnu 0.53.0",
@@ -7590,9 +7567,9 @@ dependencies = [
 
 [[package]]
 name = "zeroize"
-version = "1.8.1"
+version = "1.8.2"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "ced3678a2879b30306d323f4542626697a464a97c0a07c9aebf7ebca65cd4dde"
+checksum = "b97154e67e32c85465826e8bcc1c59429aaaf107c1e4a9e53c8d8ccd5eff88d0"
 
 [[package]]
 name = "zerotrie"
diff --git a/datafusion/substrait/Cargo.toml b/datafusion/substrait/Cargo.toml
index 16bb5cff4ad7..c1f3b47a31a3 100644
--- a/datafusion/substrait/Cargo.toml
+++ b/datafusion/substrait/Cargo.toml
@@ -37,9 +37,12 @@ chrono = { workspace = true }
 datafusion = { workspace = true, features = ["sql"] }
 itertools = { workspace = true }
 object_store = { workspace = true }
-pbjson-types = { workspace = true }
-prost = { workspace = true }
-substrait = { version = "0.58", features = ["serde"] }
+# Temporary override: substrait 0.60 requires prost 0.14 and pbjson-types 0.8,
+# but arrow-flight 56.2.0 still uses prost 0.13. Once arrow-rs releases with
+# prost 0.14 support, these can return to { workspace = true }.
+pbjson-types = "0.8"
+prost = "0.14"
+substrait = { version = "0.60", features = ["serde"] }
 url = { workspace = true }
 tokio = { workspace = true, features = ["fs"] }
 uuid = { version = "1.17.0", features = ["v4"] }
diff --git a/datafusion/substrait/src/extensions.rs b/datafusion/substrait/src/extensions.rs
index f9a2e0fb8255..079292898226 100644
--- a/datafusion/substrait/src/extensions.rs
+++ b/datafusion/substrait/src/extensions.rs
@@ -113,11 +113,15 @@ impl TryFrom<&Vec<SimpleExtensionDeclaration>> for Extensions {
 }
 
 impl From<Extensions> for Vec<SimpleExtensionDeclaration> {
+    // Silence deprecation warnings for `extension_uri_reference` during the uri -> urn migration
+    // See: https://github.com/substrait-io/substrait/issues/856
+    #[allow(deprecated)]
     fn from(val: Extensions) -> Vec<SimpleExtensionDeclaration> {
         let mut extensions = vec![];
         for (f_anchor, f_name) in val.functions {
             let function_extension = ExtensionFunction {
                 extension_uri_reference: u32::MAX,
+                extension_urn_reference: u32::MAX,
                 function_anchor: f_anchor,
                 name: f_name,
             };
@@ -130,6 +134,7 @@ impl From<Extensions> for Vec<SimpleExtensionDeclaration> {
         for (t_anchor, t_name) in val.types {
             let type_extension = ExtensionType {
                 extension_uri_reference: u32::MAX, // https://github.com/apache/datafusion/issues/11545
+                extension_urn_reference: u32::MAX, // https://github.com/apache/datafusion/issues/11545
                 type_anchor: t_anchor,
                 name: t_name,
             };
@@ -142,6 +147,7 @@ impl From<Extensions> for Vec<SimpleExtensionDeclaration> {
         for (tv_anchor, tv_name) in val.type_variations {
             let type_variation_extension = ExtensionTypeVariation {
                 extension_uri_reference: u32::MAX, // We don't register proper extension URIs yet
+                extension_urn_reference: u32::MAX, // We don't register proper extension URIs yet
                 type_variation_anchor: tv_anchor,
                 name: tv_name,
             };
diff --git a/datafusion/substrait/src/logical_plan/producer/expr/mod.rs b/datafusion/substrait/src/logical_plan/producer/expr/mod.rs
index 42e1f962f1d1..912c1397566e 100644
--- a/datafusion/substrait/src/logical_plan/producer/expr/mod.rs
+++ b/datafusion/substrait/src/logical_plan/producer/expr/mod.rs
@@ -60,6 +60,9 @@ use substrait::version;
 ///
 /// Substrait also requires the input schema of the expressions to be included in the
 /// message.  The field names of the input schema will be serialized.
+// Silence deprecation warnings for `extension_uris` during the uri -> urn migration
+// See: https://github.com/substrait-io/substrait/issues/856
+#[allow(deprecated)]
 pub fn to_substrait_extended_expr(
     exprs: &[(&Expr, &Field)],
     schema: &DFSchemaRef,
@@ -85,6 +88,7 @@ pub fn to_substrait_extended_expr(
         advanced_extensions: None,
         expected_type_urls: vec![],
         extension_uris: vec![],
+        extension_urns: vec![],
         extensions: extensions.into(),
         version: Some(version::version_with_producer("datafusion")),
         referred_expr: substrait_exprs,
diff --git a/datafusion/substrait/src/logical_plan/producer/plan.rs b/datafusion/substrait/src/logical_plan/producer/plan.rs
index 7d5b7754122d..d2192ce76d52 100644
--- a/datafusion/substrait/src/logical_plan/producer/plan.rs
+++ b/datafusion/substrait/src/logical_plan/producer/plan.rs
@@ -24,6 +24,9 @@ use substrait::proto::{plan_rel, Plan, PlanRel, Rel, RelRoot};
 use substrait::version;
 
 /// Convert DataFusion LogicalPlan to Substrait Plan
+// Silence deprecation warnings for `extension_uris` during the uri -> urn migration
+// See: https://github.com/substrait-io/substrait/issues/856
+#[allow(deprecated)]
 pub fn to_substrait_plan(
     plan: &LogicalPlan,
     state: &SessionState,
@@ -45,6 +48,7 @@ pub fn to_substrait_plan(
     Ok(Box::new(Plan {
         version: Some(version::version_with_producer("datafusion")),
         extension_uris: vec![],
+        extension_urns: vec![],
         extensions: extensions.into(),
         relations: plan_rels,
         advanced_extensions: None,