diff --git a/backend/src/db/migrations/20250429203304_certificates-ca-relation-optional.ts b/backend/src/db/migrations/20250429203304_certificates-ca-relation-optional.ts
deleted file mode 100644
index 38f106731..000000000
--- a/backend/src/db/migrations/20250429203304_certificates-ca-relation-optional.ts
+++ /dev/null
@@ -1,16 +0,0 @@
-import { Knex } from "knex";
-
-import { TableName } from "../schemas";
-
-export async function up(knex: Knex): Promise<void> {
-  if (await knex.schema.hasTable(TableName.Certificate)) {
-    await knex.schema.alterTable(TableName.Certificate, (t) => {
-      t.uuid("caId").nullable().alter();
-      t.uuid("caCertId").nullable().alter();
-    });
-  }
-}
-
-export async function down(): Promise<void> {
-  // Altering back to nullable will fail
-}
diff --git a/backend/src/db/migrations/20250429203304_certificates-ca-relation-removal.ts b/backend/src/db/migrations/20250429203304_certificates-ca-relation-removal.ts
new file mode 100644
index 000000000..1413f5096
--- /dev/null
+++ b/backend/src/db/migrations/20250429203304_certificates-ca-relation-removal.ts
@@ -0,0 +1,46 @@
+import { Knex } from "knex";
+
+import { TableName } from "../schemas";
+
+export async function up(knex: Knex): Promise<void> {
+  if (await knex.schema.hasTable(TableName.Certificate)) {
+    await knex.schema.alterTable(TableName.Certificate, (t) => {
+      t.uuid("caId").nullable().alter();
+      t.uuid("caCertId").nullable().alter();
+    });
+
+    const hasProjectIdColumn = await knex.schema.hasColumn(TableName.Certificate, "projectId");
+    if (!hasProjectIdColumn) {
+      await knex.transaction(async (trx) => {
+        await trx.schema.alterTable(TableName.Certificate, (t) => {
+          t.string("projectId", 36).nullable();
+          t.foreign("projectId").references("id").inTable(TableName.Project).onDelete("CASCADE");
+        });
+
+        await trx.raw(`
+          UPDATE "${TableName.Certificate}" cert
+          SET "projectId" = ca."projectId"
+          FROM "${TableName.CertificateAuthority}" ca
+          WHERE cert."caId" = ca.id
+        `);
+
+        await trx.schema.alterTable(TableName.Certificate, (t) => {
+          t.string("projectId").notNullable().alter();
+        });
+      });
+    }
+  }
+}
+
+export async function down(knex: Knex): Promise<void> {
+  if (await knex.schema.hasTable(TableName.Certificate)) {
+    if (await knex.schema.hasColumn(TableName.Certificate, "projectId")) {
+      await knex.schema.alterTable(TableName.Certificate, (t) => {
+        t.dropForeign("projectId");
+        t.dropColumn("projectId");
+      });
+    }
+  }
+
+  // Altering back to notNullable for caId and caCertId will fail
+}
diff --git a/backend/src/db/migrations/20250429210424_certificates-update-body-and-add-secret.ts b/backend/src/db/migrations/20250429210424_certificates-update-body-and-add-secret.ts
deleted file mode 100644
index cb5e44a03..000000000
--- a/backend/src/db/migrations/20250429210424_certificates-update-body-and-add-secret.ts
+++ /dev/null
@@ -1,33 +0,0 @@
-import { Knex } from "knex";
-
-import { TableName } from "../schemas";
-
-export async function up(knex: Knex): Promise<void> {
-  if (await knex.schema.hasTable(TableName.CertificateBody)) {
-    await knex.schema.alterTable(TableName.CertificateBody, (t) => {
-      t.binary("encryptedCertificateChain").nullable();
-    });
-  }
-
-  if (!(await knex.schema.hasTable(TableName.CertificateSecret))) {
-    await knex.schema.createTable(TableName.CertificateSecret, (t) => {
-      t.uuid("id", { primaryKey: true }).defaultTo(knex.fn.uuid());
-      t.timestamps(true, true, true);
-      t.uuid("certId").notNullable().unique();
-      t.foreign("certId").references("id").inTable(TableName.Certificate).onDelete("CASCADE");
-      t.binary("encryptedPrivateKey").notNullable();
-    });
-  }
-}
-
-export async function down(knex: Knex): Promise<void> {
-  if (await knex.schema.hasTable(TableName.CertificateSecret)) {
-    await knex.schema.dropTable(TableName.CertificateSecret);
-  }
-
-  if (await knex.schema.hasTable(TableName.CertificateBody)) {
-    await knex.schema.alterTable(TableName.CertificateBody, (t) => {
-      t.dropColumn("encryptedCertificateChain");
-    });
-  }
-}
diff --git a/backend/src/db/migrations/20250429223815_certificates-project-id.ts b/backend/src/db/migrations/20250429223815_certificates-project-id.ts
deleted file mode 100644
index 556913a6b..000000000
--- a/backend/src/db/migrations/20250429223815_certificates-project-id.ts
+++ /dev/null
@@ -1,16 +0,0 @@
-import { Knex } from "knex";
-
-import { TableName } from "../schemas";
-
-export async function up(knex: Knex): Promise<void> {
-  if (await knex.schema.hasTable(TableName.Certificate)) {
-    await knex.schema.alterTable(TableName.Certificate, (t) => {
-      t.uuid("projectId").notNullable();
-      t.foreign("projectId").references("id").inTable(TableName.Certificate).onDelete("CASCADE");
-    });
-  }
-}
-
-export async function down(knex: Knex): Promise<void> {
-  // .. tbd
-}
diff --git a/backend/src/db/schemas/certificate-bodies.ts b/backend/src/db/schemas/certificate-bodies.ts
index 10171e383..75afbddbd 100644
--- a/backend/src/db/schemas/certificate-bodies.ts
+++ b/backend/src/db/schemas/certificate-bodies.ts
@@ -14,8 +14,7 @@ export const CertificateBodiesSchema = z.object({
   createdAt: z.date(),
   updatedAt: z.date(),
   certId: z.string().uuid(),
-  encryptedCertificate: zodBuffer,
-  encryptedCertificateChain: zodBuffer.nullable().optional()
+  encryptedCertificate: zodBuffer
 });
 
 export type TCertificateBodies = z.infer<typeof CertificateBodiesSchema>;
diff --git a/backend/src/db/schemas/certificates.ts b/backend/src/db/schemas/certificates.ts
index f46a86e0a..32fb89aed 100644
--- a/backend/src/db/schemas/certificates.ts
+++ b/backend/src/db/schemas/certificates.ts
@@ -24,7 +24,8 @@ export const CertificatesSchema = z.object({
   caCertId: z.string().uuid().nullable().optional(),
   certificateTemplateId: z.string().uuid().nullable().optional(),
   keyUsages: z.string().array().nullable().optional(),
-  extendedKeyUsages: z.string().array().nullable().optional()
+  extendedKeyUsages: z.string().array().nullable().optional(),
+  projectId: z.string()
 });
 
 export type TCertificates = z.infer<typeof CertificatesSchema>;