Most of the time flies come out during the warmest time of the day, so this is usually around midday until the afternoon. During these times, just let your dog stay indoors. However, as your dog still needs to go outside to play and exercise, you can either spray the repellent provided above, or you can let them out later in the day or early in the morning. Add Plants that Repel Flies. Did you know that there are certain plants that flies hate? Examples of these are Basil, Bay Trees ...