Under EU FCR 261/2004 and subsequent case law, the right to compensation due to delayed flights is calculated solely on the "time lost" at the final destination. From pp. 17–18 of this PDF (bolding mine):
vi. ‘Long delays’ at arrival
As regards ‘long delays’, the Court has ruled that passengers, including delayed passengers, may suffer from a similar inconvenience as passengers whose flight is cancelled, consisting in a certain loss of time. Based on the principle of equal treatment, passengers reaching their final destination with a delay of three hours or more are entitled to the same compensation (Article 7) as passengers whose flight is cancelled.
The Court takes the view that a delay must be assessed for the purposes of the compensation provided for in Article 7 of the Regulation, in relation to the scheduled time of arrival at the passenger's final destination as defined in Article 2(h) of the Regulation, which in the case of directly connecting flights must be understood as the destination of the last flight taken by the passenger.
In other words, you will not be eligible for compensation if you arrive at your final destination less than three hours late.
However, you are probably still eligible for "care" (meals, refreshments, etc.), as these duties are triggered by delayed departure, not delayed arrival.
3.3.1. Delay at departure
Under Article 6(1) of the Regulation, where the departure of a flight is delayed, passengers affected by this delay have the right to ‘care’ according to Article 9, and to reimbursement and a return flight according to Article 8(1)(a).