In the period between 1997and 1999, Alkaloid, being a leader in the region and wider, was among the first companies in the region that certified the Quality Management Systems of its Profit Centers (Pharmaceuticals, Chemicals, Cosmetics and Botanicals), in accordance with the international ISO 9001 standard. In 2000-2001, Alkaloid AD Skopje was already the first company in Macedonia (Republic of North Macedonia since 2019) to be awarded with certificates for Environmental Management Systems that conform to the international ISO 14001 standard for the profit centers Botanicals and Pharmaceuticals. All ISO certificates were issued by the certification body Quality-Austria (former ÖQS) and accredited by IQNet -The International Certification Network.

In 2002, Alkaloid started its new factory for production of solid oral dosage forms, built in compliance with the European and international GMP requirements. As a confirmation for this compliance was the obtainment of the first GMP certificate that any Macedonian producer of drugs has ever been awarded with by the Macedonian Ministry of Health. At the same time, Alkaloid also received a GMP certificate for its new factory for production of cephalosporins in compliance with the national regulations, the EU 2001/83/ЕС and 2003/94/ЕС Directives and WHO Guidelines.

Starting in 1998, the Botanicals program was verified with the first certificate in organic production methods as compliant with the EU 2092/91 Directive by the Control Union Certifications (former SKAL)-Netherlands, which is the first of this kind on the Balkans. The international significance of the certificates for organic production methods is confirmed on three continents by verification according to The National Organic Programme of United States Department of Agriculture and Organic JAS-Japanese Agricultural Standards by the Control Union Certifications-Netherlands.

The production of medical devices – concentrated solutions for hemodialysis and X-ray film – the Chemicals program was awarded with CE certificates in 2007-2010 by the renowned notification body DEKRA Certification B.V. (former KEMA Quality B.V) from Netherlands. In 2011, the Chemicals– Medical Devices Program from the profit center of Chemicals Cosmetics Botanicals of Alkaloid AD Skopje obtained a Quality Management System Certificate for introduction and fulfillment of the ISO 13485 Standard requirements.

Confirmation of the commitment of Alkaloid AD "Health above all", is the HACCP certificate for production of safe food, awarded on 17.04.2007 to the Botanicals plant for the entire production program: teas, additives, spices, dried vegetables, salt and "Zachinal", issued by Quality Austria.

In 2009, Alkaloid CONS DOOEL obtained both Quality and Environmental Management Certificates in accordance with the international ISO 9001 and ISO 14001 standards.

Alkaloid d.o.o. Belgrade and Alkaloid Veledrogerija d.o.o. Belgrade successfully certified its IMS in accordance with the international ISO 9001 and ISO 14001 standards in 2012.

The first matrix Audit of Alkaloid’s Integrated Management System (IMS) was carried out by Quality Austria in 2012 and confirmed its conformity with the international ISO 9001 and ISO 14001 standards (100% of production facilities and processes) for ALKALOID AD, ALKALOID CONS DOOEL, ALKALOID d.o.o. BELGRADE and ALKALOID VELEDROGERIJA d.o.o. BELGRADE, the conformity with ISO 13485 for the profit center of Pharmaceuticals and the Chemicals program, as well as complete adherence to HACCP’s principles and requirements for the Botanicals program and PC Pharmacy.

The care for the environment is one of the long-term principles of Alkaloid AD – Skopje’s business policy, therefore the environmental management system is part of its integrated management system. In 2012 the Ministry of Environment and Physical Planning awarded the PC Pharmacy site in Avtokomanda with an A - permit for conformity with operational plan for integrated pollution prevention and control, including Alkaloid among the corporate responsible companies that, in the course of their production operations, care about the integrated prevention and control of pollution of the environment.

In 2020, Alkaloid AD Skopje strengthened its leadership position by obtaining a Certificate for compliance with the international ISO 45001 standard requirements.