MES, WMS, QMS & ERP — Systems Architecture for Regulated Manufacturing

This topic is part of the SG Systems Global regulatory & operations glossary.

Updated November 2025 • MES vs ERP vs WMS vs QMS, MOM, SCADA, paperless manufacturing, production scheduling, work-order execution, ISA-95, integration patterns • Food, Meat & Sausage, Bakery, Dietary Supplements, Pharma, Devices, Cosmetics, Chemicals, Ingredients & Dry Mixes

MES, WMS, QMS & ERP are thrown around like everyone agrees what they mean. They don’t. In many plants the result is predictable: ERP tries to run the shop floor, MES is reduced to an electronic logbook, WMS is a label-printing add-on, and QMS is a SharePoint graveyard of PDFs.

For regulated manufacturing, you can’t afford that mess. You need a clear division of responsibilities: one system owns execution and batch records, one owns inventory and locations, one owns quality and governance, one owns finance and commercial flows—and they all talk to each other without stepping on each other’s toes.

“If every system is ‘kind of’ doing everything, nothing is really under control. Good architecture is about saying: this system does this job, and here’s how they connect.”

1) The reference model — ISA-95 in plain language

Your glossary already references ISA-95 Enterprise–Control System Integration. In simple terms, it defines levels in a manufacturing stack:

• Level 4 – ERP / business planning. Long-term planning, orders, finance, high-level inventory, customers and vendors.
• Level 3 – MES / MOM. Manufacturing Operations Management: dispatching, detailed scheduling, batches, work orders, quality operations, maintenance coordination.
• Level 2 – SCADA / DCS. SCADA, DCS and HMI systems supervising equipment and lines in real time.
• Level 1 – PLCs, devices. Controllers, drives, sensors and actuators.

WMS straddles levels 3 and 4 (operational vs financial inventory), and QMS floats across levels 3–4 (governance of processes, records, risk). The whole point of ISA-95 is to stop every system trying to be every level at once.

2) MES — the execution and batch record engine

MES (Manufacturing Execution System) is Level-3’s main character. It should own:

• Work-order execution. Turning planned orders into executable jobs, routes and work-order execution sequences.
• Recipes & parameters. Implementing products & formulas, BOMs, master recipes and parameter enforcement on the shop floor.
• Process & quality data. Capturing CPPs, IPCs, deviations, signatures and attaching them to batches.
• Batch records & eBMR. Producing the BMR / eBMR or device-level DHR/eDHR.
• Genealogy. Maintaining lot & batch genealogy across process stages.

In V5, MES is where “paperless manufacturing” happens: paperless manufacturing is not just PDFs; it’s guided workflows, enforced steps and captured decisions.

3) WMS — the lot, bin & warehouse control layer

WMS (Warehouse Management System) should own the physical side of inventory:

• Location model. Warehouse locations & bin/zone topology define rooms, aisles, racks, bins, zones.
• Bin control. Bin location management ensures bins, pallets and racks are tracked as inventory positions.
• Lot & status. Lot-level quantities, expiry, QA status (hold/release), and batch-to-bin traceability.
• Directed put-away & picking. Directed put-away and directed picking enforce FEFO/FIFO and zoning with scanners, not memory.
• Cycle counting & inventory accuracy. Cycle counting and inventory accuracy functions keep the system aligned with reality.

ERP can show “we have 10,000 kg of X on site.” WMS knows “we have 6 pallets of lots A and B in these 3 bins; two pallets are on hold; one pallet is in staging.” MES uses that detail when staging material and recording consumption.

4) QMS — the governance & risk brain

QMS (Quality Management System) is less about executing a process and more about governing how processes are defined, changed and improved:

• Documents & SOPs. Document control for SOPs, WI, policies and forms, including MES/WMS configuration specs.
• Change control. Change control for recipes, processes, equipment, systems and suppliers.
• Deviations & CAPA. Nonconformances, CAPA, root-cause analysis and effectivity checks.
• Risk management. Quality risk management (QRM), FMEA, PFMEA.
• Training & competency. Training matrices and competency records.
• Audits & management review. Internal audits, supplier audits and management review cycles.

QMS doesn’t “run the line”; it defines how the line should be run, how deviations are handled and how improvements are sustained. MES/WMS provide the data; QMS governs how that data is used to make changes and decisions.

5) ERP — finance, orders & the general ledger

ERP (Enterprise Resource Planning) is where the business lives:

• Financials. General ledger, accounts payable/receivable, fixed assets.
• Purchasing & suppliers. POs, vendor master, price lists, landed costs.
• Sales & customers. SOs, customer master, pricing, tax, invoicing.
• High-level inventory & costing. On-hand per item per site, valuation, COGS, MRP.
• Basic manufacturing & planning. In some ERPs: simple BOMs, routings, demand/supply planning.

ERP is not designed to orchestrate batches step-by-step, control line speeds or manage bin-level inventory. It does not know about CPPs, IPCs, traceability graphs or CPV. That’s why trying to make ERP behave like MES/WMS/QMS leads to brittle customisations and audit pain.

6) SCADA, PLCs & paperless manufacturing — where bits hit steel

SCADA systems and PLCs live at levels 1–2:

• PLCs & control. Implement basic control logic: start/stop, PID loops, interlocks, alarms.
• SCADA/HMI. Visualise line status, let operators adjust setpoints and acknowledge alarms.

MES should consume events and data from SCADA/PLCs and send high-level commands (e.g., start batch X with recipe Y), but it doesn’t replace them. Paperless manufacturing lives at the MES/QMS layer: replacing paper travellers and logbooks with electronic workflows and signatures that still respect, and integrate with, SCADA/PLC control loops.

7) Production scheduling — who decides what runs where, and when?

Production scheduling usually straddles ERP and MES:

• ERP-level planning. MRP, capacity planning, S&OP, rough-cut plans by week or day per line or site.
• MES-level scheduling. Detailed finite-capacity scheduling and job queues for lines and work centres, considering changeovers, allergen sequences, campaign rules and cleaning.

ERP should not try to micromanage shift-by-shift sequencing; MES has the real-time visibility and constraints (equipment, training, cleaning status, material availability) to do that. V5 MES sits squarely here, taking ERP’s plan and turning it into executable, traceable work orders.

8) Integration patterns — how these systems should talk

Once you accept clear roles, integration patterns become much simpler:

• ERP ↔ MES. ERP sends planned orders (item, quantity, due date); MES returns actual production, scrap, consumption summaries and statuses. No low-level recipe logic in ERP.
• ERP ↔ WMS. ERP sends POs and SOs; WMS returns receipts, shipments and inventory adjustments aggregated by item and site.
• MES ↔ WMS. MES requests material staging and records consumption by lot; WMS fulfils picks, updates bin-level inventory and validates lot/staging rules.
• MES ↔ QMS. MES triggers deviations, change-control items and training events; QMS feeds back approved changes, risk assessments and CAPA actions.
• MES/WMS ↔ LIMS. MES and WMS provide lot/batch/sample context; LIMS returns results and statuses that drive hold/release decisions.

In V5, the V5 Connect API is the integration surface that lets V5 act as MES+WMS+QMS against an ERP like SAP, D365 or QuickBooks—without forcing ERP to know about bins, scales, CPPs or smokehouse racks.

9) How V5 implements MES + WMS + QMS around ERP

V5 Traceability is explicitly designed to occupy the Level-3 & warehouse space:

• V5 MES. Executes recipes, controls weighing & batching, captures CPPs/IPCs, builds eBMR/eDHR and genealogy, manages work-order execution and detailed scheduling.
• V5 WMS. Manages lots, bins, zones, directed put-away/picking, batch-to-bin traceability, cycle counting and outbound staging.
• V5 QMS. Owns document control, change control, deviations, CAPA, training, risk management, supplier quality and complaint handling, linked to MES/WMS data.
• V5 Connect. Integrates V5 with ERP (including QuickBooks) and specialist tools (LIMS, historians, label systems, AI analytics) via clean APIs.

This lets ERP focus on what it’s good at—finance, orders, high-level planning—while V5 handles operational reality on the plant and warehouse floor.

FAQ — MES, WMS, QMS & ERP Architecture

Q1. Can ERP replace MES, WMS and QMS if we customise it enough?
Technically, you can bolt on anything. Practically, heavy customisation turns ERP into a fragile monolith that is hard to validate, upgrade and audit. MES, WMS and QMS are specialised for execution, warehouse and quality use cases and are much better fits for regulated environments. Let ERP be the ledger; let V5 handle operations.

Q2. Where should we start if we only have ERP and spreadsheets today?
Start by picking one scope where ERP clearly struggles—e.g., batch records, lot traceability or bin-level inventory. Introduce V5 MES (for execution and batch records) or V5 WMS (for inventory) in that scope, integrate it with ERP via V5 Connect, and use early wins to justify broader rollout. Avoid “big bang” rip-and-replace projects if you’re resource-constrained.

Q3. How do we explain MES vs ERP to non-technical management?
A simple analogy: ERP is your bank and accounting system; MES is your factory’s cockpit and black box recorder. ERP knows who you billed and what you bought; MES knows exactly how each batch was made, by whom, on what equipment, under what conditions, with which lots. Both are essential; they do different jobs.

Q4. What’s the role of QMS if MES and WMS already have workflows and approvals?
MES and WMS workflows operationalise the current approved way of working. QMS defines, changes and improves those ways of working. When something goes wrong or needs to change, QMS drives the investigation, risk assessment, decision and training; MES/WMS implement the result. They are complementary, not duplicates.

Q5. Can WMS live inside MES or should it be separate?
There’s no single answer. In some plants, WMS functionality is tightly integrated into MES (like V5’s combined MES+WMS) because shop-floor and warehouse operations are highly intertwined. In others, a stand-alone WMS makes sense. The key is function, not labels: lots, bins and directed movements must be handled by something appropriate and integrated, whether or not it’s a separate product.

Q6. How do we avoid integration turning into a fragile spider web?
Keep each system’s responsibilities clear; use standardised interfaces (APIs, ISA-95-style integration objects); minimise point-to-point custom scripts; and centralise orchestration where it makes sense. V5 Connect exists specifically to reduce brittle integrations by giving ERP, LIMS and external systems a single, documented way to talk to MES/WMS/QMS.

Related Reading (Glossary)
• Core Systems: MES | WMS | QMS | ERP | MOM
• Architecture & Control: ISA-95 | ISA-88 | SCADA | Paperless Manufacturing | Production Scheduling | Work-Order Execution
• V5 Platform: V5 Solution Overview | V5 MES | V5 WMS | V5 QMS | V5 Connect API