Optimizing nutrient management in organic polytunnel production remains challenging due to the limited availability of field-based knowledge on the mineralization dynamics of organic fertilizers. At the same time, microalgae-based products such as Chlorella vulgaris have gained increasing attention in recent research, yet their interactions with nutrient supply intensity are not well understood. This study aimed to evaluate the effects of increasing nutrient supply intensities (34, 116, and 189 kg ha⁻¹ N from different organic sources), in combination with C. vulgaris foliar application, on the crop performance of kapia pepper and a subsequent leafy green crop under on-farm organic polytunnel conditions on soil with moderate organic matter content. Increasing production intensity did not result in significant improvements in pepper yield or vegetative biomass (p > 0.05), and no significant residual effects of nutrient supply were detected in the yield of the subsequent leafy green crop (p: 0.08–0.94). C. vulgaris treatment showed predominantly non-significant but positive trends in several parameters, but only in combination with high-intensity technology, while reducing the total pest damage of the thrips and stinkbug index up to 15.7% in most technology variations. These results indicate that the effects of C. vulgaris may be strongly context-dependent and confirm that increasing the intensity of nutrient supply may carry the risks of conventionalization of organic farming practices.