In breeding the best genotypes for diverse conditions, ideally the breeder should test all his crossings under all these conditions. Especially with complex physiological traits like yield, which exhibit large variation, this would require many expensive and large field trials. The EU project “Smart tools for Prediction Improvement of Crop Yield” (SPICY) aims at the development of a suite of tools to help breeders in predicting phenotypic response of genotypes for complex traits under a range of environmental conditions. Pepper is used as a model crop. The primary tool to be developed is an integrated gene-to-phenotype model, which integrates the approaches of QTL and crop growth modelling. To generate data to develop and validate these models, a recombinant inbred line (RIL) population of Capsicum annuum ‘Yolo Wonder’ × ‘Criollo de Morelos 334’ was phenotyped at two sites (Netherlands and Spain) and in two seasons (spring and autumn). Phenotyping was done both manually by measuring characteristics like fruit set and development rate, and by newly developed image analysis and fluorescence tools permitting high throughput phenotyping of dynamic trait expression. In the analysis of the data, the complex trait yield was analysed in the components contributing to the total fresh fruit yield. The results of the phenotyping experiments will be used as input in the crop growth models. The genotype-to-phenotype model, combination of crop growth models and QTL analysis tools which will be developed in the EU-SPICY project will be able to predict phenotypic response based on genetic information.