Pesticide Residue Testing: Overcoming Tolerance Level Challenges

Pesticide residue testing has become a critical priority for food and beverage companies across North America as regulatory frameworks tighten, global sourcing increases, and consumer demand for transparency continues to grow. Agencies such as the U.S. Environmental Protection Agency (EPA), USDA, and Canada’s Pest Management Regulatory Agency (PMRA) continuously update Tolerance Levels, placing significant compliance responsibilities on manufacturers, importers, and retailers. At the same time, the European Food Safety Authority (EFSA) continues to apply even stricter standards, complicating cross-border trade.

For companies operating in this environment, the ability to rapidly and accurately test for pesticide residues is essential not only to meet compliance obligations but also to protect brand reputation and consumer trust. Mérieux NutriSciences supports the industry with ISO 17025-accredited chemistry services, advanced instrumentation, and consultative expertise to design programs that align with both domestic and international regulations. This blog explores the most recent trends in pesticide residue monitoring, highlights the challenges posed by shifting Tolerance Levels and global supply chains, and demonstrates how Mérieux NutriSciences partners with food and beverage stakeholders to navigate these complexities.

Current Trends in Pesticide Residue Testing in Food

Regulatory Shifts and Tolerance Levels Requirements

Regulatory expectations in North America are evolving in response to advancements in science and shifting public health priorities. The USDA’s most recent Pesticide Data Program reported that more than 99% of tested foods complied with EPA tolerances in 2023, underscoring both strong compliance and the ongoing need for vigilant residue testing programs (USDA, 2024).

However, alignment with international markets remains a challenge. EFSA’s monitoring program reveals that the European Union enforces stricter and more precautionary Tolerance Levels standards than North America, creating hurdles for companies seeking dual market access (EFSA, 2023). These differences mean that food and beverage producers must not only ensure compliance with domestic rules but also anticipate requirements abroad.

As regulators expand the number of pesticides under surveillance, laboratories must maintain flexible methods that can adapt to hundreds of analytes. While automation and machine learning tools assist in managing these large datasets, industry experts emphasize that human chemist oversight remains critical for validation and accurate interpretation of results (SelectScience, 2023). 

Import Surveillance and Detentions

Global trade continues to elevate the risk of regulatory detentions. According to FoodChain ID, import non-compliance rates in the EU are up to five times higher than for domestic products due to stricter enforcement and diverse agricultural practices across supplier regions (FoodChain ID, 2025). The same risks apply to U.S. and Canadian markets, where imported produce, grains, and processed goods are routinely tested.

Border detentions not only disrupt supply chains but also damage brand trust. Companies that implement proactive import screening programs—designed around commodity type, supplier history, and emerging violation trends—can significantly reduce the likelihood of costly disruptions (FoodChain ID, 2024a). 

Commodity Risk Patterns

Some commodities consistently demonstrate elevated pesticide residue risk. USDA monitoring highlights produce, grains, baby foods, teas, and spices among the most vulnerable categories, due to either frequent pesticide application or heightened consumer sensitivity (USDA, 2024).

These commodities also present analytical challenges. For example, botanicals and processed products often contain complex sample matrices that can interfere with analytical methods, requiring specialized expertise to ensure accurate results (SelectScience, 2023). As consumer markets diversify and regulatory authorities broaden their testing scope, laboratories must continue validating methods across a growing spectrum of food and beverage categories.

Evolving Chemistries and Emerging Analytes

The pesticide landscape is not static. Public scrutiny continues around well-known compounds, such as glyphosate and neonicotinoids, while regulators also track new chemistries and potential contaminants. Laboratories are responding with greater adoption of high-resolution mass spectrometry (HRMS), which enables both targeted and non-targeted analysis as well as retrospective data review when regulations shift (SelectScience, 2023).

Modern workflows increasingly rely on LC-MS/MS and GC-MS/MS platforms combined with QuEChERS extraction. These approaches allow laboratories to detect hundreds of residues in a single run while handling diverse food matrices (SepScience, 2023). Such technologies ensure that testing programs remain both comprehensive and adaptable as new pesticides come under regulatory review. 

Speed-to-Market Pressures and Turnaround Time

Today’s food and beverage companies cannot afford long testing delays. Seasonal product launches, just-in-time supply chains, and competitive retail environments demand fast turnaround times (TAT) for residue testing. Laboratories that implement multi-residue “mega-methods” and intelligent instrument automation can deliver results faster while maintaining regulatory-grade reproducibility (SelectScience, 2023; Mérieux NutriSciences, 2024).

For many companies, this balance between speed and accuracy is the difference between capturing or missing a market window. Partnering with laboratories that can scale testing volume and adjust TAT options according to client needs is now a strategic advantage. 

Supply Chain Complexity and Risk-Based Testing

Globalization has expanded sourcing networks, but it has also introduced new risks. Variations in agricultural practices, pesticide application rates, and regulatory oversight across regions mean that companies must carefully manage supplier relationships. A risk-based testing program—tailored to commodity type, origin, and supplier reliability—is now considered best practice (FoodChain ID, 2024a).

By integrating chemical expertise, data analytics, and supply chain insights, companies can focus testing resources where risks are greatest while maintaining compliance across diverse product lines.

How Mérieux NutriSciences Supports Pesticide Residue Testing in Food

ISO 17025 Accreditation and Method Validation for Food Pesticide Testing

Mérieux NutriSciences operates a network of ISO 17025-accredited laboratories, ensuring international standards of accuracy, precision, and defensibility. Methods are validated against evolving Tolerance Levels to ensure sensitivity at or below regulatory thresholds, providing clients with confidence that results will withstand regulatory scrutiny (Mérieux NutriSciences, 2024). 

Advanced Multi-Residue and Targeted Analytical Techniques

Using advanced LC-MS/MS and GC-MS/MS instrumentation, Mérieux NutriSciences offers multi-residue methods capable of screening hundreds of analytes in a single run. The laboratories employ QuEChERS workflows to optimize sample preparation, ensuring consistency across commodity groups such as produce, botanicals, and processed foods (SepScience, 2023; SelectScience, 2023). 

Matrix Expertise and Consultative Program Design

Beyond analytical execution, Mérieux NutriSciences provides consultative expertise to design risk-based testing programs. Teams advise on sampling frequency, matrix-specific challenges, supplier geography, and corrective action plans. This integrated approach enables companies to move from reactive testing to proactive risk management (SelectScience, 2023).

Turnaround Time, Flexibility, and Data Integrity

Recognizing the importance of supply chain agility, Mérieux NutriSciences offers both standard and rush testing services. Results are accompanied by comprehensive chain-of-custody documentation to support regulatory filings and incident response. This flexibility ensures that clients can align testing schedules with commercial priorities while maintaining complete data traceability.

Import Screening and Compliance Assurance

With regulatory agencies focusing on imported commodities, Mérieux NutriSciences assists clients in developing import screening programs aligned with current violation trends. By identifying risks before goods reach borders, companies reduce the likelihood of detentions and protect continuity of supply (FoodChain ID, 2025). 

Expert Perspectives on the Future of Pesticide Residue Testing

Industry experts agree that the scope of pesticide testing will continue to expand. As analyte lists grow, high-resolution mass spectrometry is becoming increasingly valuable for capturing both known and unknown residues (SelectScience, 2023). Despite advances in automation and AI-driven data processing, human chemists remain essential for data interpretation and validation.

In addition, laboratories are adopting more sustainable practices by reducing solvent usage, minimizing plastic waste, and incorporating climate adaptation strategies into method design (SelectScience, 2023). These initiatives reflect not only operational efficiency but also alignment with broader sustainability goals across the food and beverage sector.

Frequently Asked Questions on Pesticide Residue Testing in Food

Q1. How often should I test for pesticide residues across different commodities? Testing frequency depends on commodity type, supplier risk, and regulatory requirements. Mérieux NutriSciences helps design risk-based programs that align with USDA, EPA, and PMRA standards.

Q2. How does North American compliance differ from the EU? North American tolerances (EPA, USDA, PMRA) are generally less restrictive than EU limits, which can complicate exports. Our chemistry experts provide cross-market compliance strategies to reduce detention risk.

Q3. What turnaround times are possible for multi-residue analysis? Our ISO 17025-accredited labs offer both standard and rush services, balancing regulatory-grade accuracy with the speed required for just-in-time supply chains.

Q4. What’s changing in pesticide regulations in 2024–2025? Shifts include lower Tolerance Levels for specific commodities, growing scrutiny of glyphosate and neonicotinoids, and increased import surveillance (FoodChain ID, 2025; EFSA, 2023). 

Get Started with Pesticide Residue Testing in Food Today

The landscape of pesticide residue testing in food in North America is shaped by evolving regulations, heightened scrutiny of emerging analytes, and increasingly complex supply chains. Food and beverage companies must balance speed, accuracy, and compliance while maintaining consumer trust and global market access.

Mérieux NutriSciences provides the technical expertise, validated methods, ISO accreditation, and consultative program design needed to help clients navigate this environment with confidence. By implementing tailored, multi-residue testing programs supported by advanced instrumentation, companies can protect brand equity, ensure compliance, and safeguard public health. Learn more about our pesticide residue testing services or get started with a pesticide testing kit today!

References

EFSA. (2023). Annual report on pesticide residues monitoring. EFSA Journal. https://www.efsa.europa.eu/en/efsajournal/pub/9398

FoodChain ID. (2024a, June 10). Pesticide tolerance levels: Recent challenges and violations. https://www.foodchainid.com/resources/pesticide-mrls-challenges-violations/

FoodChain ID. (2025, February 4). A closer look at global pesticide residue incidents in 2024. https://www.foodchainid.com/resources/pesticide-residue-incidents-2024/

SelectScience. (2023). Leading pesticide analysis experts tackle the challenges and future outlooks of residue testing. https://www.selectscience.net/article/leading-pesticide-analysis-experts-tackle-the-challenges-and-future-outlooks-of-residue-testing

SepScience. (2023, December 7). Challenges and solutions while performing pesticide analysis for the food and beverage industry. https://www.sepscience.com/pesticide-analysis-food-and-beverage-company-6481

USDA. (2024, November 10). USDA testing for 2023 shows 99 percent of foods do not exceed pesticide residue tolerances. https://www.food-safety.com/articles/9895-usda-testing-for-2023-shows-99-percent-of-foods-do-not-exceed-pesticide-residue-tolerances