diff --git a/src/config/backends/config-txt.ts b/src/config/backends/config-txt.ts
index 4eb46f9a..d4f2c17f 100644
--- a/src/config/backends/config-txt.ts
+++ b/src/config/backends/config-txt.ts
@@ -219,7 +219,11 @@ export class ConfigTxt extends ConfigBackend {
 		// Split dtoverlays from their params to avoid running into char limits
 		// and write at the end to prevent overriding the base overlay
 		if (opts.dtoverlay != null) {
-			for (const entry of opts.dtoverlay) {
+			for (let entry of opts.dtoverlay) {
+				entry = entry.trim();
+				if (entry.length === 0) {
+					continue;
+				}
 				const [overlay, ...params] = entry.split(',');
 				confStatements.push(`dtoverlay=${overlay}`);
 				confStatements.push(...params.map((p) => `dtparam=${p}`));
@@ -245,9 +249,16 @@ export class ConfigTxt extends ConfigBackend {
 	public processConfigVarValue(key: string, value: string): string | string[] {
 		if (isArrayConfig(key)) {
 			if (!value.startsWith('"')) {
+				if (key === 'dtoverlay' && value.trim().length === 0) {
+					return [];
+				}
 				return [value];
 			} else {
-				return JSON.parse(`[${value}]`);
+				const res: string[] = JSON.parse(`[${value}]`);
+				if (key === 'dtoverlay') {
+					return res.filter((s) => s.trim().length > 0);
+				}
+				return res;
 			}
 		}
 		return value;
diff --git a/src/config/utils.ts b/src/config/utils.ts
index 04ccd1d6..04bdf0d2 100644
--- a/src/config/utils.ts
+++ b/src/config/utils.ts
@@ -33,6 +33,7 @@ export function envToBootConfig(
 		.mapValues((val, key) =>
 			configBackend.processConfigVarValue(key, val || ''),
 		)
+		.pickBy((val) => !Array.isArray(val) || val.length > 0)
 		.value();
 }
 
diff --git a/test/integration/config/config-txt.spec.ts b/test/integration/config/config-txt.spec.ts
index 8ac6814e..667f0003 100644
--- a/test/integration/config/config-txt.spec.ts
+++ b/test/integration/config/config-txt.spec.ts
@@ -306,4 +306,55 @@ describe('config/config-txt', () => {
 
 		await tfs.restore();
 	});
+
+	it('ignores empty dtoverlay on the target state', async () => {
+		const tfs = await testfs({
+			[hostUtils.pathOnBoot('config.txt')]: stripIndent`
+	        enable_uart=1
+					dtparam=i2c_arm=on
+					dtparam=spi=on
+					disable_splash=1
+					dtparam=audio=on
+					gpu_mem=16
+					`,
+		}).enable();
+
+		const configTxt = new ConfigTxt();
+
+		await configTxt.setBootConfig({
+			dtparam: ['i2c=on', 'audio=on'],
+			dtoverlay: [''],
+			enable_uart: '1',
+			avoid_warnings: '1',
+			gpu_mem: '256',
+			initramfs: 'initramf.gz 0x00800000',
+			'hdmi_force_hotplug:1': '1',
+		});
+
+		await expect(
+			fs.readFile(hostUtils.pathOnBoot('config.txt'), 'utf8'),
+		).to.eventually.equal(
+			stripIndent`
+					dtparam=i2c=on
+					dtparam=audio=on
+					enable_uart=1
+					avoid_warnings=1
+					gpu_mem=256
+					initramfs initramf.gz 0x00800000
+					hdmi_force_hotplug:1=1
+				` + '\n',
+		);
+
+		// Will try to parse /test/data/mnt/boot/config.txt
+		await expect(configTxt.getBootConfig()).to.eventually.deep.equal({
+			dtparam: ['i2c=on', 'audio=on'],
+			enable_uart: '1',
+			avoid_warnings: '1',
+			gpu_mem: '256',
+			initramfs: 'initramf.gz 0x00800000',
+			'hdmi_force_hotplug:1': '1',
+		});
+
+		await tfs.restore();
+	});
 });
diff --git a/test/integration/device-config.spec.ts b/test/integration/device-config.spec.ts
index c2e437b0..1de55b6c 100644
--- a/test/integration/device-config.spec.ts
+++ b/test/integration/device-config.spec.ts
@@ -228,6 +228,30 @@ describe('device-config', () => {
 			expect(logSpy).to.not.be.called;
 		});
 
+		it('ignores empty dtoverlay when comparing current and target state', async () => {
+			const current = {
+				HOST_CONFIG_initramfs: 'initramf.gz 0x00800000',
+				HOST_CONFIG_dtparam: '"i2c=on","audio=on"',
+				HOST_CONFIG_foobar: 'baz',
+			};
+			const target = {
+				HOST_CONFIG_initramfs: 'initramf.gz 0x00800000',
+				HOST_CONFIG_dtparam: '"i2c=on","audio=on"',
+				HOST_CONFIG_dtoverlay: '',
+				HOST_CONFIG_foobar: 'baz',
+			};
+
+			expect(
+				// @ts-expect-error accessing private value
+				deviceConfig.bootConfigChangeRequired(
+					configTxtBackend,
+					current,
+					target,
+				),
+			).to.equal(false);
+			expect(logSpy).to.not.be.called;
+		});
+
 		it('writes the target config.txt', async () => {
 			const current = {
 				HOST_CONFIG_initramfs: 'initramf.gz 0x00800000',