Abstract Efficient cargo delivery is essential for plant trait engineering, yet existing methods are often species-specific and ineffective across diverse habitats. Here, we develop core-shell microneedles for targeted delivery of biomolecular cargoes and active microorganisms into both terrestrial and aquatic plants. The microneedle architecture is rationally engineered to resist water exposure and release cargo upon contact with plant interstitial fluid, enabling controlled delivery into tissues and cells. We demonstrate that these core-shell microneedles can efficiently transport diverse cargoes, from nanoscale biomolecules such as functional nucleic acids, proteins, and plant hormones to microscale bioactive Agrobacterium , leading to strong protein expression and enhanced plant growth. Underwater delivery of salt-tolerance genes into submerged freshwater plants further demonstrates the platform’s utility for engineering stress resilience in challenging environments. By facilitating the cellular uptake of diverse cargoes into intact plants across different habitats, this amphibious microneedle strategy offers a versatile cargo delivery tool to advance plant biotechnology and environmental applications.