Curly top disease caused by geminiviruses including Beet curly top virus (BCTV) and Beet curly top Iran virus (BCTIV) is a limiting factor for sugar beet production. In recent years, climate change has increased the spread of virus vectors and disease damage in infected regions. The most economical control of BCTV in sugar beet would be through resistant cultivars though, most commercial cultivars possess only low to moderate resistance. A doubled haploid Line KDH13 showed resistance to BCTV and produced no symptoms. However, the response of Line KDH13 to BCTIV was not studied before. Here we tested the response of Line KDH13 to the BCTIV infection and compared with BCTV infection by means of inoculation with infectious clones mobilized by agrobacteria. Real-time PCR showed that both viruses replicated in the locally agroinfiltrated cotyledons. The viral DNA accumulation was lower for BCTIV compared to the BCTV infection. Systemically infected resistant plants with BCTV showed mild enation without leaf curling after 30 days. In contrast, leaf curling appeared after 12 days in the susceptible line. Further, BCTIV was not detected in resistant plants. Transcriptome analysis for the BCTV infected plants showed only 43 genes that were deregulated in line KDH13 compared to the regulation of a large number of genes (1139 gene) in the susceptible line. This work demonstrates the response of sugar beet plants to BCTV / BCTIV infection at both local and systemic infection and highlight the metabolic pathways/defense-related genes for their contribution towards BCTV resistance.