Transposable elements (TEs) are major components of plant genomes, profoundly impacting the fitness of their hosts. However, technical bottlenecks have long hindered our mechanistic understanding of TEs. Using RNA-Seq and long-read sequencing with Oxford Nanopore Technologies’ (ONT) direct cDNA sequencing, we analyzed the heat-induced transcription of TEs in three natural accessions of Arabidopsis thaliana (Cvi-0, Col-0, and Ler-1). In addition to the well-studied ONSEN retrotransposon family, we confirmed Copia-35 as a second heat-responsive retrotransposon family with particularly high activity in the relict accession Cvi-0. Our analysis revealed distinct expression patterns of individual TE copies and suggest different mechanisms regulating the GAG protein production in the ONSEN versus Copia-35 families. In addition, analogously to ONSEN, Copia-35 activation led to the upregulation of flanking genes such as APUM9 and potentially to the quantitative modulation of flowering time. ONT data allowed us to test the extent to which read-through formation is important in the regulation of adjacent genes. Unexpectedly, our results indicate that for both families, the upregulation of flanking genes is not predominantly directly initiated by transcription from their 3′ long terminal repeats. These findings highlight the intraspecific expressional diversity linked to retrotransposon activation under stress.