diff --git a/Core/MIPS/IR/IRFrontend.cpp b/Core/MIPS/IR/IRFrontend.cpp
index 08667325f1..d98b49dbc5 100644
--- a/Core/MIPS/IR/IRFrontend.cpp
+++ b/Core/MIPS/IR/IRFrontend.cpp
@@ -313,7 +313,8 @@ void IRFrontend::DoJit(u32 em_address, std::vector<IRInst> &instructions, u32 &m
 		instructions.reserve(block_instructions.size() + 2); // +2 for Downcount and LogIRBlock
 		// The first instruction is "Downcount"
 		instructions.push_back(block_instructions.front());
-		instructions.push_back({ IROp::LogIRBlock, {0}, 0, 0, 0 });
+		// prepare_block() fills in the constant, unless it fails to record the block.
+		instructions.push_back({ IROp::LogIRBlock, {0}, 0, 0, INVALID_TRACE_INDEX });
 		std::copy(block_instructions.begin() + 1, block_instructions.end(), std::back_inserter(instructions));
 	}
 
diff --git a/Core/MIPS/MIPSTracer.cpp b/Core/MIPS/MIPSTracer.cpp
index 27e62892a0..a04d00c2ff 100644
--- a/Core/MIPS/MIPSTracer.cpp
+++ b/Core/MIPS/MIPSTracer.cpp
@@ -113,10 +113,20 @@ bool MIPSTracer::flush_to_file() {
 		return false;
 	}
 	auto trace = executed_blocks.get_content();
+	int skipped = 0;
 	for (auto index : trace) {
+		// Blocks compiled before an earlier flush (or before a clear) still carry their old index,
+		// which no longer refers to anything. Clearing the jit cache gets rid of them for good.
+		if (index >= trace_info.size()) {
+			skipped++;
+			continue;
+		}
 		auto& block_info = trace_info[index];
 		flush_block_to_file(block_info);
 	}
+	if (skipped != 0) {
+		WARN_LOG(Log::JIT, "Skipped %d stale block(s) in the trace, clear the jit cache to avoid this", skipped);
+	}
 
 	INFO_LOG(Log::JIT, "Trace flushed, closing the file...");
 	fclose(output);
diff --git a/Core/MIPS/MIPSTracer.h b/Core/MIPS/MIPSTracer.h
index d9c873323d..6741929c7c 100644
--- a/Core/MIPS/MIPSTracer.h
+++ b/Core/MIPS/MIPSTracer.h
@@ -29,6 +29,9 @@
 #include "Common/Data/Collections/CyclicBuffer.h"
 
 
+// Stored in the LogIRBlock instruction's constant field for a block the tracer never recorded.
+constexpr u32 INVALID_TRACE_INDEX = 0xFFFFFFFF;
+
 struct TraceBlockInfo {
 	u32 virt_address;
 	u32 storage_index;